The Age of Paradox: Book One- History of Paradox
by Marcus S. Lazarus
Summary: In a world where the Time War ended quite differently, the newly-regenerated Doctor crash-lands into Amelia Pond's life after two lifetimes of solitude, and finds the one person who may help him learn how to be what he once was in the face of a nightmare
1. The Policeman Comes

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: While the changes may appear subtle at first, this is set in an alternate universe where the Time War happened quite differently from the version we know in canon; how it diverged from what we know is something you'll find out over time, but pay close attention to the fine details and you might find some clues...

AN 2: Thanks are owed to WickedForGood13, whose story 'Keeping Faith' inspired some later elements of this story- they'll feature in the first few chapters, so that's not a significant spoiler- and whose worth as a second opinion on this story is unquestionably appreciated

**The Age of Paradox: **

**Book One:**

**The History of Paradox**

Amelia Pond, aged seven, had already come to the conclusion that life was not fair.

She hated the fact that she'd had to leave Scotland and come all the way down the Leadworth for reasons that not even she could remember, she hated the way that Aunt Sharon varied between ignoring her and expecting her to be all proper and quiet when she had people over, she hated the fact that the children at school kept staring at her and whispering about her when they thought she couldn't hear them...

Most of all, she hated the fact that she _knew _that there was something wrong with everything around her, but she just couldn't work out _what _it was.

Maybe it was the fact that, whenever she tried to think of what had happened to her parents, the only thing she could clearly recall- apart from vague impressions of comforting smiles and reassuring hugs- was a sharp flash of what looked almost like bone, as though something made of that had hit her...

She knew that it was stupid, but she just couldn't shake the feeling that something had been _wearing _that bone when... it happened.

It was enough to make her think of the tales she'd heard when her parents thought that she was asleep... the rumours and fears of the Faction who hid behind everything...

She didn't know where those stories came from, but Amelia couldn't remember a time when she _hadn't _been scared of the Faction; the tales of the men in bone, whispered rumours and theories that she'd heard when nobody thought she was paying attention or when the older boys and girls at school didn't know that she was there... the men who'd been there when things went wrong...

She'd never heard more than vague details, but what she had heard had always scared her; everything she heard reminded her of the tale of the mice and the bell that her mother had once told her, where everyone had a plan or theory about how to deal with the cat but nobody had the courage to actually do anything about it, except that nobody was even sure where to get a bell to help them in the first place.

And then...

Amelia couldn't help but shudder as she glanced at the crack on her bedroom wall.

She didn't care what Aunt Sharon said about the crack just being damaged plaster that she couldn't be bothered fixing; there was something _wrong _with that crack, even if she didn't know what.

Maybe it was the whispers she heard sometimes when nobody else was in the house, or maybe it was something about the way she sometimes felt it looking at her, or maybe it was just the fact that she dreamed such strange dreams whenever she fell asleep near it- dreams of a woman screaming and calling her name as she fell through... _something_... along with some kind of robot dog-, but whatever it was, there was definitely _something _about that crack that wasn't normal.

On impulse, Amelia got out of bed, knelt down on the edge, and clasped her hands together as she shut her eyes.

It might be stupid, but with Aunt Sharon intent on ignoring the crack, it was all that she could think of to try; if Aunt Sharon wouldn't do anything, she'd turn to the one person who _hadn't _let her down yet.

"Dear Santa," she said solemnly, "thank you for the dolls, and the pencils, and the fish. It's Easter now, so I hope I didn't wake you, but... honest, it is an emergency."

She paused for a moment to glance over at the crack on her wall- that strange, unusual crack, looking almost like a smile as it stood out from her otherwise smooth wall-, before she continued speaking.

"There's a... crack in my wall," she continued, feeling a need to elaborate on the reason why she was troubling him with something so apparently trivial. "Aunt Sharon says it's just an ordinary crack, but I know it's not, because... at night there's voices. So please, please could you send someone to fix it. Or a policeman. Or..."

She trailed off as she heard a strange sound coming from the back garden, just outside her window- a wheezing, groaning, whooshing sound, as though something was exerting a great deal of effort to get somewhere-, followed by a loud crash as something was apparently smashed.

"Back in a moment," Amelia said, hoping that Santa wouldn't mind the interruption as she hurried over to the window and pushed the curtain aside. Her eyes immediately fell on what had to be the source of the noise; a large box, apparently a dark colour of some sort that Amelia couldn't quite identify in the darkness, lying on its side amid the shattered remains of what had been Aunt Sharon's garden shed, a series of small illuminated windows around what looked like the top of the box-

Amelia's eyes instantly focused on one of the words written at the top of the box.

_Police_.

"Thank you, Santa," she whispered, glancing upwards in gratitude at his prompt response to her prayer, before she turned around to grab her dressing-gown and torch and hurry down the stairs, pausing only briefly to pull on her red wellies before she opened the door and ran through the garden towards the still-steaming police box. For a moment, she could only stare uncertainly at the box as she got closer to it- how was anyone meant to get out of it if it had landed like this-, but then her question was answered as two doors on what was probably its front if it was standing upright suddenly burst open, releasing a fresh burst of steam.

As Amelia stared incredulously at the sight, a rope with some kind of hook on the end emerged from the box, latching on to one of the nearby pieces of gardening equipment that Aunt Sharon always kept in the shed, followed shortly afterwards by a hand grabbing onto the edge of the box that was facing Amelia. Another hand appeared just moments after the first one, and then a head emerged from the box, brown hair soaking wet on top of an almost rectangular face that was grinning widely at her.

"Can I have an apple?" he said, looking optimistically at her. "All I can think about; _apples_. I love apples. Maybe I'm having a craving! That's new, never had cravings before."

Amelia wasn't sure what she could say to that, so simply stood in silence as this strange man hauled himself out of his box, revealing a blue shirt and brown trousers that looked like they had sustained various rips and tears at some point- he gave a rather raggedy impression, all things considered- as he sat on the edge of the box and looked into the doors.

"Woooah!" he said, as though there was something impressive inside the small box. "Look at that!"

"Are you OK?" Amelia asked at last, uncertain what else could be said in this situation.

"Just had a fall," the man said, shrugging slightly as he looked back at her. "All the way down there, right to the library. Hell of a climb back up."

"You're soaking wet," Amelia said, indicating the rest of his body with her torch; she was starting to doubt that Santa had sent such a strange man to help her problem.

"I was in the swimming pool," the man replied, swinging one leg around to sit on the edge of the box as he reached up to adjust his shirt collar.

"You said you were in the library," Amelia pointed out.

"So was the swimming pool," the man replied, as though that was just something that happened to him rather than something completely bizarre.

"Are you a policeman?" Amelia asked.

"Why?" the man replied, leaning forward slightly to look at her. "Did you call a policeman?"

"Did you come about the crack in my wall?" Amelia asked.

"What cra-?" the man began, only to suddenly yell in pain as he fell off his box and fell to the ground, bent over as he clutched at his chest in pain.

"You all right, Mister?" Amelia asked, stepping forward slightly to look at him, usual warnings about strangers forgotten as she looked at this strange man; something about the innocent way he'd smiled at her after emerging from the box made her fairly sure that he wasn't going to hurt her.

He might have arrived under strange circumstances, but he couldn't belong to the Faction; they were too... _old_, and this man was so young.

"Yeah, I'm fine, it's OK..." the man said, nodding reassuringly at her even as his hands clutched at his chest. "This is all perfectly nor-!" he was cut off as his body violently jerked forward, followed by his mouth opening and something floating out of his mouth, making Amelia briefly wonder if he'd swallowed a swarm of fireflies for some reason before the bright light faded.

"Who are you?" she asked, looking back at the man in confusion as he held out his hands in front of him, his hands briefly glowing with the same stuff that had just come from his mouth.

"I don't know yet," he said, grinning at her. "I'm still cooking..."

Amelia wondered what he meant by that; did he mean that he'd been 'made' by the box or something like that? The way it had opened with all that steam _did _resemble an oven...

"Does it scare you?" he asked,

"No," Amelia replied, shaking her head firmly at him- whatever else she was, Amelia Pond was _not _a coward; the Faction might scare her, but she wouldn't let that be all she was-, smiling slightly to back her statement up. "It just looks a bit weird-"

"No no no," the man said, looking at her with a soft smile, "the crack in your wall; does it scare you?"

"Yes," Amelia admitted.

As though that had been the cue he was waiting for, the man grinned and leapt to his feet, Amelia taking a step or two back at the sudden change in height; she hadn't realised just how tall he was when he was sitting down.

"Well then, no time to lose!" the man said, grinning at her. "I'm the Doctor; do everything I tell you, don't ask stupid questions, and don't wander off."

Before Amelia could say anything to those orders, the man- the Doctor- turned around and walked into the nearest tree with a prominent smacking sound, falling backwards to land on the ground near Amelia's feet.

"You all right?" Amelia asked, standing uncertainly over him.

"Early days," the Doctor- somehow Amelia knew that was how he'd pronounced it; the _Doctor_, no other name needed- said, smiling briefly back at her. "Steering's a bit off."

Before Amelia could ask what he'd meant by that, the Doctor was back on his feet, smiling at her once again. "First things first; what have you got to eat?"

* * *

><p>AN 3: No obvious differences in <em>what <em>they're doing so far, I admit, but have patience; things _will _change soon, and there's still Amelia's thoughts about her past to consider...


	2. The Crack

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: I've skipped over the scenes involving the Doctor discarding Amelia's prior food suggestions, but this begins as he's eating the fish custard; hope you like it

AN 2: Again, changes are subtle, but pay attention; the little details _will _add up before I present the bigger picture...

The History of Paradox

As the Doctor stood in the house, looking at the little girl sitting opposite him as he chewed on the fish finger dipped in custard currently in his mouth, he didn't know why he was staying here for so long.

OK, so the TARDIS had taken a few knocks after he was nearly caught following that whole mess with trying to shut down the Gate- you'd think that even _they _would know now to tamper with that kind of thing; even with his currently-depleted resources, he wasn't going to ignore something like _that _on Earth-, but he could go somewhere more private to let the old girl recuperate; he didn't have to sit around here and experiment with his new mouth and whatever food this little Scottish girl had to offer...

Then again, he supposed he couldn't shake the truth of the matter; he might not want company after what had happened to Fitz and Compassion- and that mess with Jack hadn't helped matters much-, but that didn't mean he didn't enjoy the opportunity to make a few new friends.

Besides, after the way she'd so casually accepted such a bizarre introduction to her life- he hadn't even managed to change his shirt yet-, the Doctor had to confess that he was curious about this girl before him; he'd thrown away or spat out everything she'd offered him before now, he'd come into her life out of thin air- destroying what looked like a garden shed in the process-, he'd expelled regenerative energy in front of her, he hadn't given her a name beyond 'the Doctor'...

And she'd just _accepted _him, trusting that he wouldn't hurt her, showing no fear in the face of the strange and inhuman things he'd done so far...

It was moments like this- _people _like this- that reminded the Doctor why he loved Earth so much; groups could be a bother at times, but people could still surprise you if you let them.

On impulse, the Doctor lifted the bowl of custard in front of him and drank it- he felt in the mood for something a bit different from simple water-, putting it down after he'd swallowed his fill, wiping away the gathering substance he'd felt on his upper lip as he looked casually at the girl.

"You're funny," the girl said, smiling at him.

"Am I?" the Doctor said, relieved to hear it; 'funny' was always better than 'creepy' in the early days of a new body. "Good... funny's good. What's your name?"

"Amelia Pond," the girl replied.

"Oh, that's a brilliant name," the Doctor said, smiling in approval at her. "Amelia _Ponnnd_. Like a name in a fairytale."

The warm smile the girl gave him in response assured him that he'd said the right thing; it might have been centuries since he'd been a father, but some instincts never went away.

"Are we in Scotland, Amelia?" he asked, realising that he still didn't have any idea where he'd landed apart from that he was still on Earth.

"No," Amelia replied with a frustrated sigh as she picked at her food. "Had to move to England. It's rubbish."

"So what about your mum and dad then?" the Doctor asked, chewing on another fish finger as he glanced upwards. "Are they upstairs? Thought we'd've woken them by now."

"Don't have a mum and dad," Amelia replied, her expression sadder as she spoke. "Just an aunt."

"I don't even have an aunt," the Doctor said, smiling at her as he swallowed the fish finger in his mouth.

"You're lucky," Amelia said, smiling at him.

"I know," the Doctor said; he might not like being alone, but at least now he didn't have to worry about Quences or the other Cousins trying to tell him what to do with his life...

"So, your aunt," he said, turning the attention to more immediate matters (Those days might have long gone even before the Time War, but the knowledge that he'd never see Innocet or the like again was far from comforting). "Where's she?"

"She's out," Amelia said.

"And she left you all alone?" the Doctor said, his eyes widening at this news as he pulled the fish finger he'd just been about to eat out of his mouth, taking the custard off as he did so.

"I'm not scared!" Amelia said, looking indignantly at him.

"'Course you're not!" the Doctor said, smiling at her confirmation of his own assessment of her. "You're not scared of anything! Box falls out of the sky, man falls out of the box, man eats fish custard, and look at you! Just sitting there."

The slight smile that Amelia gave him in return was all he needed to confirm that he'd said the right thing.

"So you know what I think?" he added, the compliment out of the way as he chewed on another fish finger.

"What?" Amelia asked.

"Must be one hell of a scary crack in your wall," the Doctor said grimly, putting down his food as he looked resolutely at her, all joviality gone in face of this new mystery; whoever or whatever he was, he was the Doctor, and he would _never _back down from someone who needed him.

_Not in _this _timeline, anyway_... that treacherous part of his mind reminded him, but he forced that down as he headed up the stairs, following Amelia's direction to her room at the other end of the corridor up the stairs (Why a 'family' consisting of one child and her aunt had such a large house didn't immediately make sense to the Doctor, but he'd worry about that later; this crack was the problem right now).

"You've had some cowboys in here," he said reflectively as he studied the crack on the wall of the room- a simple child's room, but even the simple coloured pencils and models were a welcoming sight of the warmth he'd never really enjoyed as a child-, glancing back at her as a random, potentially regeneration-influenced thought occurred to him. "Not actual cowboys, though that can happen."

"I used to hate apples," Amelia said as she stood at the door, a reflective tone to her voice. "Then my mum put faces on them."

Glancing back, the Doctor couldn't help but feel slightly touched as she walked over to him and held another apple up to him, a simple smiling face on one side of it.

"She sounds good, your mum," the Doctor said, tossing the apple into the air before catching it and slipping it back into his pocket. "I'll keep it for later."

Turning his attention back to the wall before him, the Doctor walked over and studied the crack more carefully, running his fingers over it as he thought.

"This wall is solid and the crack doesn't go all the way through," he said after a brief analysis, checking the crack with his fingertips one last time to confirm his findings about what kind of architecture he was dealing with. "So here's the thing; where's the draft coming from?"

Standing back from the wall, he gave it a quick scan with the sonic screwdriver before he stepped back, glancing at the result of the analysis on the screwdriver.

"Wibbly wobbly timey wimey," he muttered thoughtfully to himself before he slid the screwdriver shut and looked at Amelia. "Do you know what the crack is?"

"What?" Amelia asked, shaking her head slightly uncertainly.

"It's a crack," he said, staring at the wall with Amelia for a moment before he pressed his face up against the crack, tapping his fingers lightly on the area around it to get a better feel for the anomaly before he voiced his findings to Amelia. "But I'll tell you something funny; if you knock this wall down, the crack would stay put, 'cause the crack isn't in the wall."

"Where is it, then?" Amelia asked.

"Everywhere," the Doctor replied, still staring at the crack; he'd seen temporal rifts in the past, but never something like this...

"In everything," he continued, looking thoughtfully at the crack as his fingers danced across. "It's a split in the skin of the world. Two parts of space and time that should never have touched... pressed together. Right here in the wall of your bedroom."

On impulse, he pressed his ear up against the crack and listened, glancing back at Amelia as a faint rumble of some sort reached his ear. "Sometimes- can you hear-?"

"A voice," Amelia finished for him. "Yes."

Noting a glass on her bedside table, the Doctor hurried over to pick it up, throwing the water aside- he would have preferred a stethoscope, but his jacket had been too tight after he regenerated and he didn't know where his coat was in the mess that the control room had been in- and pressing the open end against the crack, putting his ear to the other end of the glass.

"_Prisoner Zero has escaped_," a voice said on the other end of the crack.

"Prisoner Zero..." the Doctor repeated thoughtfully.

"Prisoner Zero has escaped," Amelia repeated. "That's what I heard. What does it mean?"

The Doctor didn't answer at first, but continued to listen through the glass, only to step back after he had confirmed that whatever voice was on the other side of the crack had nothing else to say.

"It means," he said, stepping back from the wall and putting the glass to one side as he looked at the crack, "on the other side of this wall, there's a prison, and they've lost a prisoner, and d'you know what that means?"

"What?" Amelia asked.

"You need a better wall," he said; he might have gone into more detail in his last body, but he had a feeling this incarnation would be more 'to-the-point' in a crisis.

"The only way to close the breach is to open it all the way," he continued, dragging the desk that was pressed against the wall out of the way; he wasn't entirely sure what would happen if he did this, and he didn't want Amelia to lose anything if it didn't go completely according to plan. "Forces will invert, and it will snap itself shut... or..."

"What?" Amelia asked.

"You know when grown-ups tell you everything's gonna be fine, and you think they're probably lying to make you feel better?" the Doctor asked, looking uncertainly at Amelia.

"Yes," Amelia said, in a tone that suggested she was used to this kind of treatment.

"Everything's gonna be fine," the Doctor said, out of a lack of anything else to say; he was fairly sure he knew what he was doing, but this kind of crack was still a mystery...

To take his mind off that possibility, he held out a hand to Amelia, smiling slightly as she took it, moving her into position behind him as he turned his attention back to the wall. Flicking the sonic screwdriver on to a different setting, he aimed his tool at the crack and activated it, the crack glowing with a brilliant white light before it opened- he hoped that Amelia didn't compare it to a mouth; the last thing he wanted was to give her nightmares that this thing was going to come back and eat her-, revealing a black void with bars vaguely visible in the distance.

"_Prisoner Zero has escaped_," the voice the Doctor had heard earlier said again, this time significantly clearer than it had been. Stuck for anything else to do as the voice repeated itself, the Doctor took a tentative step forward, taking care to keep Amelia behind him as he did so; he didn't _think _anything could get through this crack in the time it would take for everything to invert, but if so he was better equipped to cope with whatever they had to throw at him than Amelia was.

"Hello?" he called out uncertainly. "Hellooo...?"

As though in response to his call, something that looked like a large eyeball appeared on the other side of the crack, looking around the room before it focused on the two of them as the Doctor took a tentative step forward. Before he could decide on the appropriate verbal response, the creature fired a glowing ball of light that curved to hit the Doctor's pocket, knocking him off-balance and striking Amelia's bed. Briefly disorientated by the surprise impact, the Doctor only had enough time to see the crack close after he regained his balance, Amelia's wall now smooth once more.

"There, see!" he said, smiling over at Amelia. "Told you it would close; good as new?"

"What's that thing?" Amelia asked, looking anxiously at him. "Was that Prisoner Zero?"

"No... I _think _that was Prisoner Zero's guard," the Doctor said, reaching into his pocket and pulling out his psychic paper (How he'd lost track of this for so long after Serena's death he didn't know, but he couldn't imagine how he'd get by without it these days). "Whatever it was, it sent me a message; psychic paper, takes a lovely little message."

Opening the wallet, he studied the paper, only to be disappointed at the brevity of the message; he'd been hoping for new information, but all he had was the same thing he'd heard already.

"'Prisoner Zero has escaped'," he read from the paper, getting back to his feet as he slipped the paper back into his pocket. "But why tell us? Unless..."

"Unless what?" Amelia asked, apprehension clear in her voice.

"Unless Prisoner Zero escaped through here," the Doctor said, studying the room around him; maybe Prisoner Zero was some kind of time-shifter- a Vecton sprung to mind, but there was no sign of the distinctive buzzing they made-, only to be met with nothing. "But he couldn't have; we'd know."

Hurrying out of the room, he scanned the surrounding landing, trying to determine if there was something here he should be aware of- this house was large, but the landing was relatively empty; there had to be _something _here that hadn't been there earlier, hadn't he learned enough to always take in his surroundings with history the way it was these days?-, fighting to remain focused through the post-regenerative disorientation.

"It's difficult," he said, noting Amelia looking at him with a simple concern he had to confess he'd missed; he'd spent so long serving as the leader in a crisis situation that he'd rarely met anyone who cared about _him _personally, apart from that brief reunion with Sarah and that short time he'd spent travelling with Jack after rescuing him. "Brand new me, nothing works yet, but there's something I'm missing... in the corner... of my eye..."

The Doctor didn't know what he'd sensed, but there was definitely something off to the side- probably behind that door at the end- that wasn't _quite _right; if he could just look at it the right way, he _might _be able to figure out what it was about it that was nagging at his regeneration-disorientated mind (This was the clearest he'd been post-regeneration for a while, but he knew that he was having _some _trouble focusing)...

Then the ominous sound of a bell came from the garden, and the Doctor's attempt to place this anomaly were forgotten

"No, no no no no no no, noo!" he yelled, running down the stairs and out into the garden, barely aware of Amelia's short form as she hurried after him.

"I've gotta get back in there!" the Doctor yelled by way of explanation; he might only have a few theories about what was happening to the TARDIS, but after the damage it had taken before this last landing none of them were good. "The engines are phasing! It's gonna burn!"

"But... it's just a box," Amelia asked, looking sceptically at him as he hurried to pick up the grapple and rope he'd used to leave the ship earlier. "How can a box have engines?"

"It's not a box," the Doctor said, picking up the last of the rope before he looked at her with a broad smile; even after everything else that had happened, he loved seeing the moment when he could introduce a whole new world to someone else's perceptions. "It's my time machine."

"What?" Amelia asked, looking at him with renewed scepticism. "A real one? You've got a real time machine?"

"Not for much longer, if I can't get it stabilised!" the Doctor replied, looping the rope around the right door-handle; he'd have to pull the doors shut himself if this was going to work. "Five minute hop into the future should do it!"

"Can I come?" Amelia asked after a brief pause, looking at him with a hopeful smile.

_I shouldn't_...

The Doctor knew that he'd made that vow to himself for a good reason- something to do with Fitz, he knew _that _much-, but for the life of him, he couldn't recall _what _it had been...

When he looked at little Amelia Pond, standing there, looking at him with her hopeful smile, the Scottish girl in an English village, no family, no reference to friends, unafraid of being alone but scared of the crack in her wall, so accepting of the strange man who fell out of the sky in a box...

He couldn't leave her life like this.

"Not safe in here, not yet," he said, looking at her with a brief apology that would have to suffice until he could give her something better, looping the rope around the left door-handle as he spoke. "Five minutes. Give me five minutes! I'll be right back."

"People always say that," Amelia said, staring sullenly at the ground as she spoke, her tone reflecting a world-weariness that no child should possess at that age.

"Am I people?" the Doctor said, his planned leap forgotten as he hopped down from the edge of the TARDIS and walking over to crouch down in front of Amelia, looking her directly in the eyes as he spoke. "Do I even look like people?"

For a moment, the two stared at each other, and then the Doctor gave her a brief, small smile, allowing himself to feel a slight spark he hadn't felt since that dark day when he'd lost so much. "Trust me... I'm the Doctor."

Amelia's smile wasn't much, but it was what he needed to see before he turned his attention back to the matter at hand. Hurrying back to the TARDIS, he hopped up to sit on the edge, glanced back to take a last look at Amelia, and then leapt downwards into his already-shifting ship, the rope clutched in his hand as he pulled the doors closed behind him, landing on the console as he took a quick assessment of the situation.

From what he could see, it looked like it was trying to reconfigure itself to repair the damage while still keeping itself stable enough for him to use- the old girl knew how he'd felt about company recently and was probably trying to give him the chance to leave-, but he wasn't going to take the easy way out and go somewhere else; he'd promised Amelia that he'd come back, and he _would _be back for her.

Even as he set the coordinates for a short hop a few metres to the left and a short distance into the future, he could only hope that the temporal systems were fully operational...

* * *

><p>AN 3: It's after this that things begin to <em>really <em>diverge from what you've seen, although there are still some differences in the past that you'll need to learn about as time goes on (As for _how _things will change in the next chapter, I'll just say that it's a less drastic jump forward this time around)...


	3. Seven Years Later

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: I took some inspiration for this chapter- and the original idea for this story, actually- from WickedForGood13's story "Keeping Faith", and use them with her permission

AN 2: As always, note the clues; things are going to get _very _interesting as things go on...

The History of Paradox

At seven years old, Amelia Pond had concluded that life wasn't fair.

At fourteen years old, she was becoming ever more firmly convinced that it was true.

Here she was, still stuck in the same boring town with the same frustratingly negligent aunt- she liked the freedom she got living with Aunt Sharon, but would it be asking too much to feel like someone actually cared about her for _her_ sake rather than just because of what her condition said about Aunt Sharon?-, looked down on as that strange girl with the fixation on her imaginary friend by virtually every one of her peers, ahead on her subjects when she cared to study and caught up even on the things she didn't like, with the result that it was a weekend, and she didn't have a thing to do.

Oh, Rory and Mels were all right for company, but Mels's 'enthusiasm' for the Doctor was a bit too much at times- she believed that the Doctor tried to help people, but it seemed a bit much for Mels to blame all major historical disasters on the idea that he hadn't been there, particularly when she seemed to focus more on what the Doctor _did_ rather than who he _was_-, and Rory sometimes seemed to just tolerate her stories about him rather than anything else; he seemed to think that she should have gotten past that belief by now...

But she couldn't just... _dismiss_ what had happened; even with her nightmares having died down since the crack had gone, even without her fears that the Faction were watching her- she still had the occasional nightmare, but it was nothing more than the odd flash, like what she'd read about in _Harry Potter_ when he was dreaming about his parents' deaths-, she couldn't forget that strange, raggedy man, who'd come crashing into her life as he was 'born' from his police box to eat her food and fix her wall as though it was nothing exceptional but just another day in his obviously-remarkable life...

Despite what Mels seemed to think, what made the Doctor so extraordinary was that he _wasn't_ extraordinary; he was strange, and he acted oddly, and he claimed to have a time machine- which she _seriously_ doubted, although that was just the part of her that wanted him to come back; if he'd cared, couldn't he have gone back already?- but when you got past the fact that he had a time machine and he was so apparently cleverer than anybody else, he really wasn't that far from normal; just a lot more willing to listen to the fears that she'd always dismissed as too childish to tell to anyone else and so much more willing to listen to her problems than other adults...

_But he'd left her._

That was the part where all her best intentions and desire to think the best of the Doctor fell apart, really; he'd left her, and, no matter what kind of stuff he had, he'd never come back for her.

She'd waited out in the garden all night- she didn't remember who'd brought her back afterwards, but she knew she'd fallen asleep out there-, she'd waited out there every night for the next few weeks- despite Aunt Sharon trying to bring her back inside- until it became too cold, she'd told everyone about her strange encounter with the Guarding Eye and the Raggedy Doctor...

And he'd _never_ come back for her.

He'd completely changed everything she thought she knew about adults and people by accepting her fears and listening to her as an equal- that 'everything's going to be fine' moment didn't count; he'd all but admitted that he was lying before he said it anyway-, and then he'd vanished without a trace, leaving her to more irregular but no less disturbing nightmares about the Faction over the years, sometimes about her parents and sometimes about other things (God, she even thought she remembered dreaming about unicorns on the Golden Gate Bridge at one point; what was _wrong_ with her mind?).

She _wanted_ to think the best of him, but she just couldn't bring herself to go that far; he'd shaken everything she thought she knew, and left her with nothing but a smooth wall and the same old random nightmares-

The sound of a wheezing, groaning noise cut off her train of thought, leaving her to stare incredulously at the garden in front of her as wind began to blow around her from out of nothing.

As she stared incredulously at the sight appearing before her eyes, the wheezing was suddenly accompanied by the sight of a tall blue box fading into existence, its wooden panels clear in a manner that they'd never been in any of her old dreams of his return- she'd made the box so many shades of blue in her stories and pictures, but somehow _this_ blue was suddenly the only blue that it could have ever been and she didn't know how she could have made such a mistake earlier-, until it solidified with a firm _thump_ and the door opened, revealing the same brown-floppy-haired man in raggedy clothes that she'd first seen all those years ago, coughing as smoke followed him out of the door of his ship.

"Amelia!" the Doctor yelled, shutting the door behind him as he hurried towards the house, running past her as she stared in shock at this new arrival. "I've worked out what it was! I know what I was... missing..."

His initial rush faltered as he registered the other presence in the garden for the first time, prompting him to stop as he turned to look at the young red-haired girl standing before him, a stern glare on her face as she did so. "Amelia?"

"Hello, _Doctor_," Amy said, folding her arms as she glared at him, her stance only relaxing slightly as she took in the faint trace of orangish crumbs on his shirt, apparently in the same area where they'd been left when he originally left her house all those years ago.

It didn't make up for _everything_, of course, but it was possible...

If he still had those crumbs on him, than it was possible that he hadn't lied to her or betrayed her at all; it was just possible that he was a really, really, _really_ bad driver.

"I'm a little late, aren't?" the Doctor said, drawing her out of her possible thoughts of forgiveness and focusing her mind back on her current anger.

"Seven years," Amy said, glaring at him; accidental delays or not, she wasn't going to let him off that easily.

"Oh," the Doctor said, looking suddenly embarrassed as he glanced back at his ship. "Uh... sorry about that; I _did _mean to only go forward five minutes, but the engines were phasing; I must have gone a bit far..."

"Seven years," Amy said, her voice as cold as she could make it while resisting the urge to just break down and cry with relief at the sight of him.

"I didn't do it on _purpose_-" the Doctor protested weakly.

"Seven years, and Aunt Sharon's trying to get me to see my _fourth _psychiatrist," Amy interjected.

"_Fourth_?" the Doctor repeated incredulously.

"I keep biting them," Amy clarified, a slightly embarrassed tone to her voice as she looked slightly away from the Doctor. "They said you weren't real."

"Ah," the Doctor said, nodding in understanding before he smiled in approval at her. "Good for you; never be afraid to tell authority when it's wrong-"

"_You left me_!" Amy yelled, hurling herself at the Doctor as she beat her fists against his chest, the blows send the Doctor staggering back slightly until his back was pressed against the door of the box, tears of rage and sorrow on Amy's face as she glared at him. "I _waited _for you and you _left me_!"

"I didn't do it on purpose-!" the Doctor said once again.

"_Seven years_ of being the weird kid with the 'imaginary friend' telling tales about her doctor to the other kids; do you _know _what that's like?" Amy asked, grabbing the Doctor's tie and yanking it down to glare at him; a part of her mind couldn't believe that she was doing this to an adult, but something about the Doctor made him seem a lot younger than he looked even as it made him seem older at the same time, so that conventions of generational interaction didn't apply to him. "Everyone telling me I was weird, Aunt Sharon wondering how I broke the shed, my only friend wondering why I kept talking about you even after we stopped playing dress-up, and then there was all those nightmares about the Faction-"

"The _Faction_?" the Doctor said, his eyes widening in sudden horror as he placed his hands on her shoulders to push her back, crouching down slightly so that he could look her directly in the eyes. "They're _here_?"

"Well... I mean, I've dreamed about men in bone once or twice; who _else _could it be?" Amy said, looking at him with a sudden uncertainty; she'd seen the Doctor confident and in control back when he'd confronted the crack in her wall, but right now he almost looked like he was fighting to stop himself from panicking...

"Back in a sec; literally don't go _anywhere_," the Doctor said, diving back into his box, followed by the faint sound of something metallic moving against something else that was made of metal before he stepped back out of the box, holding something in his hand.

"The Time Vector Generator," the Doctor explained, brandishing the object in question in front of her as he closed the door behind him; now that Amy saw it, it looked like a long bronze wand with a light on the end. "Remove this, and my time machine _is _just a box; gives the old girl a chance to repair herself without worrying about maintaining the link to her interior dimensions, and it should make it harder for the Faction to realise that I'm here..."

He trailed off for a moment, looking back at the box for a moment with an air of such deep melancholy that Amy briefly forgot about her old anger at him, before he turned back to look at her with a resolute expression, all trace of his earlier fear erased. "Come on; there's something I need to check."

"What-?" Amy asked, as he grabbed her by the wrist and hurried back into the house, heading up the stairs towards the first floor, Amy so surprised at this sudden return to a state that she could only describe to herself as a living dream that she forgot that she was meant to be angry with him.

"If I'm right," the Doctor said, pausing at the top of the stairs to look grimly at her, "Prisoner Zero should be in _here_."

"Where?" Amy asked, looking around the landing in confusion. "Are you telling me-?"

"Look," the Doctor said, staring urgently at her.

"Look where?" Amy asked, indicating the floor with a frustrated wave as another reason for his current behaviour suddenly occurred to her. "If this is some way of distracting me-"

"Look exactly where you don't want to look, where you never want to look, in the corner of your eye; _look_!" the Doctor said, staring at her with a new intensity that even her current anger at him couldn't allow her to ignore.

Slowly, uncertainly, Amy turned her head towards this slight blur in the corner of her vision, an itch in the side of her mind that she hadn't even been aware existed until the Doctor's words brought it to her attention...

Her eyes widened in shock at the sight in front of her.

There was _another _door there.

"But..." she said, shaking her head in confusion. "But I've never... how can...?"

"There's a perception filter around the room to stop you registering it; I saw it the last time I was here, but then the TARDIS engines collapsed and I couldn't stick around to investigate it further," the Doctor explained, pulling out his sonic screwdriver and aiming it at the door. "Just give me a few moments to see what we're dealing with here- I have some ideas, but confirmation's always a good thing-, and in the meantime, _stay outside_."

Even as the Doctor opened the door and cautiously walked into the room, Amy was already following behind him as silently as possible; he might have come back into her life and proven that she _wasn't _insane, but that didn't give him the right to start ordering her around after everything he'd put her through over the years.

God... the man had just _vanished _seven years ago, showed up out of the blue claiming that it was just an 'engine malfunction', and he thought _that _would be enough to get her to listen to him?

She wasn't a little girl any more, and she was going to do what _she _felt best, and right now that included going into that room after the Doctor.

Walking into the room, for a moment Amy didn't see anything in this room worth getting worked up about- it looked like the only thing stored in here were a couple of bits of furniture that was too old for the rest of the house and a couple of boxes-, but then she saw the Doctor staring at something that looked like a semi-transparent snake-like thing hanging from the ceiling and she let out a small scream of shock.

"_Get BACK_!" the Doctor yelled, his gaze still fixed on the creature in front of him as he waved a hand urgently at the door behind him, simultaneously grabbing the creature's head with his other hand. For a moment, the Doctor and the snake-thing stared at each other, totally immobilised, and then the creature's mouth opened with a roar and the Doctor staggered backwards, the hand that had been holding the creature's head held away from him as though it had been burned.

"RUN!" the Doctor yelled, pulling out that small silver thing he'd used to seal the crack- she'd taken to calling it the 'time stick' out of a lack of anything else to call it- from his pocket and aiming it at the snake-thing, leaving the snake shaking and screaming before he turned around and ran out of the door. Amy only just managed to follow him before the snake started to regain its senses, the Doctor shutting the door behind them as soon as he'd left it.

"What just-?" Amy asked.

"Just a minor bit of psychic backlash," the Doctor said, quickly aiming the silver thing at the lock while he held his head with the other hand. "Teach me to try and telepathically link up to something that isn't fully in phase with this dimension while I'm still cooking; I haven't dealt with that kind of psychic backlash since I tried to talk to the Waro..."

"What?" Amy asked, looking at him in confusion and shock before latching on to the most immediately-necessary question. "What are the 'Waro'... and what _was _that thing-?"

"Questions later; escape now!" the Doctor said, grabbing her arm and hurrying down the stairs, quickly using the stick to lock the front door behind him before he and Amy ran for the street.

"Hold on; you can't just-!" Amy said, staring impatiently at the Doctor as they ran up a road, only for the Doctor to come to a halt mid-way up the road and turn to look at her with a slightly awkward smile.

"Sorry about that; had to get you away from the multi-form before it tried to kill us," he said, smiling awkwardly at her as she caught up with him.

"Multi-what?" Amy asked.

"Multi-form," the Doctor repeated. "Well, what I picked up when I took a look like that suggested that it was one of the Faction loa, really- complex spirits manifesting in this dimensional plane, unspecified crimes against reality, using others' bodies; it meets most of the requirements, even if it's not doing the last in the usual way-, but that's not important right now; what _is _important is that it's here, and-"

"..._vacate the human residence_," a voice said, the words only just becoming audible to the Doctor and Amy as they walked up the road, "_or the human residence will be incinerated_."

"What?" the Doctor said, turning to look for the source of the voice before Amy noticed that it was coming from an ice-cream van, the speakers blaring a disturbing message in an unfamiliar deep voice rather than the usual cheery music; "_Prisoner Zero will vacate the human residence, or the human residence will be incinerated_."

"Oh no..." the Doctor said, his eyes widening in horrified understanding as he looked at the ice-cream van, its driver fiddling in frustration with the speaker's controls.

"What?" Amy asked, looking in shock at the van; it had barely been five minutes, and already everything she'd spent the last seven years trying to understand or forget- the last only occasionally, but she had been experiencing some moments of doubt as she grew up- seemed to be hitting her all at one. "Now the _ice-cream van's_ looking for Prisoner Zero too?"

"No it's not..." the Doctor said, his eyes flickering around the local area- they were near the 'Leadworth Green', as Amy had always called the large patch of grass around the centre of the village-, before he picked up a radio inside the van, ignoring the driver's sceptical looks as he held his silver stick up to it and adjusted the frequency knobs.

It didn't take long for Amy to realise what he was listening for; no matter _how _he turned the dial, it was still going on about Prisoner Zero and the incineration of the human residence.

"Oh no..." the Doctor said, glancing around the area, inspiration and horror warring for supremacy on his face as Amy watched.

"What?" she said, looking at him urgently after he'd spent a few moments in silence. "What's _wrong_?"

"The 'human residence'..." the Doctor said, looking grimly back at her, the light on his 'time stick' flicking on and off as he continued to change the radio settings only to find nothing but the request for Prisoner Zero. "If they were just referring to your house, they wouldn't feel the need to send the message all the way out here; add in the fact that, if Prisoner Zero _is _what I sensed it was, it should be capable of getting away from anything they can do to a few buildings..."

"Hold on a minute; are you saying-?" Amy began.

"They're not talking about your house, they're talking about the planet," the Doctor said, putting down the radio and walking off the down the street, Amy quickly falling into place behind him as she listened to him. "Somewhere up there, there's a spaceship... planet this size, two poles, basic molten core... they'll need a forty percent fission blast, but they'll have to power up first, so, assuming a typical fleet comprised of your average medium-sized star ships... recognising that Prisoner Zero probably can't do anything against them now but is definitely _very _dangerous... that's twenty minutes."

"Twenty minutes?" Amy repeated uncertainly. "Twenty minutes to what?"

"The end of the world," the Doctor said, looking back at her grimly. "We've got a bit of time before they establish a forcefield to contain the blast- no way of knowing how far Prisoner Zero can teleport itself, but there aren't many safe off-planet destinations in this area that anything could reach travelling that way, and a forcefield would contain the blast to the surface and ensure that Prisoner Zero can't access even those few possibilities available-, but after the forcefield's up we've got twenty minutes..."

Shaking his head, he glanced at his surroundings, a frustrated expression crossing his face as he took them in. "This is Leadworth, right?"

"Yes," Amy replied.

"And this is _it_?" he asked, looking at her in frustration. "No airport, no nuclear power station... how long to the nearest city?"

"Half an hour by car," Amy replied.

"We don't have half an hour, you're _definitely _not old enough to have a car, and I have no desire to waste time on something like that; _perfect_!" the Doctor said, groaning as he slapped a hand against his forehead in frustration. "Twenty minutes to save the world, and all I have is a shut post office- WAIT!" he said, slapping his hand against his forehead again. "What was that- when I read- when I felt- ARGH!"

Whatever he had been trying to say was suddenly cut off when he collapsed to the ground, clutching at his chest and wincing; Amy was suddenly reminded of the time he'd fallen out of his box and breathed fireflies when she'd first seen him.

"It's too soon..." he said, shaking his head in frustration as he looked up at her. "I'm not ready, I'm not _done _yet... too much, too fast... I've been alone too long..."

Something about that statement made her snap, as all the tension she'd been feeling since the Doctor revealed the presence of that additional room in her house finally found something to latch on to.

"You've been alone too long?" Amy said, grabbing him by his tattered shirt and hauling him up slightly to face her, ignoring the way a tear on the right side of his chest grew larger as she did so; this wasn't the time to consider why he hadn't changed his clothes in seven years. "_You've _been alone too long? At least you've been able to _travel _somewhere; I've been stuck in this _useless _place for _eight years _waiting for you! Where the hell have you _been_?"

"Amy, I've already told you, my ship was damaged and I went too far forward, and I am _sorry_, but right now we have more important things-!" the Doctor tried to protest, wincing for a moment before he turned his attention back to her.

"Who are you?" Amy asked firmly.

"Amy, this isn't the time, end of the world, just over _twenty minutes_-!" the Doctor began.

"Talk _quickly_," Amy said, placing as much weight on the Doctor's chest as she dared, ignoring the stares that she was attracting from some of the people passing by; at this time on a Sunday, most people were just staying indoors, and the few who were out and about weren't going to get involved in something like this unless it looked like they really _had _to.

That was people the world over, really; never paying any attention to other peoples' problems unless they absolutely _had _to-

"Catch," the Doctor suddenly said, pulling an apple out of his pocket and tossing it towards her. Amy caught it automatically, one hand grabbing the apple while the other shifted to grab the front of the Doctor's shirt as he lay on the grass-

_No_.

It was _impossible_...

It had been seven years since she'd given the Doctor an apple; _nothing _could last that long...

But there it was.

That same simple, stupid face that her mother had shown her how to carve, the feel of the apple so familiar against her fingers even after the seven years' growth they'd experienced since she held this apple- but it couldn't be- last...

"I'm the Doctor," the Doctor said, his voice soft as he looked at Amy, a pleading expression in his eyes. "I'm a time-traveller; everything I told you seven years ago is true. "I'm real, what's happening in the sky is real, and if you don't let me go right now, everything you've ever known is over."

"I... I..." Amy began weakly, staring between the apple and him for a moment before she suddenly became aware of something strange; it might be her imagination, but just around where her legs were keeping the Doctor pinned to the ground, she felt something...

Moving the hand that had been holding his shirt, Amy's fingers traced down to the left side of the Doctor's chest, feeling the rapid thump of his heart on that side, before moving slowly and uncertainly over to the other side of his chest, where a slightly _different _beat greeted her fingers.

"Two hearts..." she said, her eyes widening incredulously.

"Yes," the Doctor said, smiling softly at her, a strange, comforting smile that made her feel safe in a manner that she couldn't define- it wasn't paternal, and it wasn't totally friendly either, but she still felt... _safe_... was the only term that fit- as he reached up to take hold of her arm with one hand, indicating the apple still held in her palm. "Look at it; fresh as the day you gave it to me, and you know it's the same one."

Amy couldn't quite believe it.

Seven years of dreaming, praying, hoping, wishing, and cursing his name, and the Raggedy Doctor had come back at last, his word only broken by the most tragic of accidents, seeking her help in something so terrifying and incredible that Amy couldn't even imagine _what _they were going to do next...

She saw the world around her briefly turn darker, as though something had slightly covered the sun, but she didn't need to look directly upwards to know that something fundamental about the world around her had changed.

The Raggedy Doctor had come back, and she was _not _going to let him go this time.

"Amy," the Doctor said, looking urgently at her. "The sun is being blocked by a forcefield; we now have twenty minutes to save the world. Just... _believe _for those twenty minutes."

Nodding in resolution, Amy clambered off the Doctor and helped him back to his feet.

"What now?" she asked.

"Does Leadworth have a hospital?" the Doctor asked, smiling hopefully at her.

"Uh..." Amy replied, her enthusiasm momentarily dampened by the confusing change of topic before she remembered. "The Royal Leadworth; it's a few minutes' drive... _that _way; it's not much, but-"

"Perfect; just what Prisoner Zero needs!" the Doctor said, smiling as he grabbed her hand and ran towards a nearby car. Before Amy had time to think about what they were doing, the Doctor had used his 'time stick' to open the doors and had clambered into the driver's seat, opening the passenger door for Amy before she could even think about voicing any objections about what they were doing (Not that she would have done, anyway; she knew without needing to be told that the Doctor wouldn't _steal _something like this, but merely borrow it until he didn't need it).

"Come on, Amelia Pond!" the Doctor said, aiming his seemingly-magic silver stick- maybe she should call it the time _wand_; it certainly seemed to be cool enough- at the car's ignition. "To the Royal Leadworth!"

As the car started and the Doctor floored the accelerator, Amy didn't know what the Doctor was thinking, but she was suddenly certain that he could do it; if he could change her world with an apple and a silver stick, what _couldn't _he do seemed to be the better question right now.

She couldn't wait to tell Rory and...!

Rory and...

Amy frowned, excitement forgotten in the face of this sudden internal mystery.

Now that she thought about it, she wasn't sure why she'd started to think 'and' there; there _was _no 'and' after Rory.

Actually, when she put a bit more thought into it, she wasn't sure she even wanted to tell Rory about it; the idea of him and the Doctor meeting just felt... _off_, was the best term she could think of-

Then the Doctor rounded a corner and drove onto a bypass with a loud cry of "_Geronimo_!", and thoughts of Rory vanished from Amy's mind.

The fate of the world was in the hands of her and her Raggedy Doctor; everything else seemed so... _irrelevant_ right now...

* * *

><p>AN 3: Anyone notice that little twist at the end?<p>

Trust me, that's going to be VERY relevant later...


	4. Containing the Prisoner

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Hope you like this chapter; capturing the Doctor's mental state at this point was _not _as simple as you'd assume- to say nothing of the need to adjust his solution to stop Prisoner Zero based on the fact that technology's slightly less advanced than it was in the 'actual' course of events (Keep in mind that he's going after Prisoner Zero five years before he did in the show)-, but I like to think I did an OK job

The History of Paradox

As he drove towards the Royal Leadworth, the Doctor was trying not to think about what had just happened- rematerialising seven years late and thus eliminating any possibility that he could have just safely 'cut' Amelia out of his life like he had everyone else he'd met since things went wrong-, even as a part of him that he'd tried to deny for so long cursed the fact that he had missed so much of her life; a few simple mistakes as the engines reorganised the systems after the damage he'd accidentally caused in his last regeneration, and suddenly he was dealing with a teenager who'd spent half her life waiting for him?

He should have just gone with his first instincts and left her completely alone rather than stick around for food and that crack; after she'd spent so long waiting for him, how was he meant to leave her again after he'd let her down so drastically already without making her feel even _more _disappointed?

_Maybe you don't have to..._

He _had _to leave her; it wasn't _safe _to be around him any more! He'd realised how foolish he was being about 'abandoning' companions to protect himself following Lucie's death after he found himself coincidentally back at the rally where he'd left Sam- a few bad experiences didn't change the fact that he _did _make people better- look at how well Steven, Nyssa and Benny had done after he'd left them!-, but this wasn't like it had been back then; after the War ended in the first strike- and _especially _after what Fitz and Compassion had done to keep him safe-, he _couldn't _put anyone else at risk...

_That never stopped you before_...

Being on the run from the Time Lords who would have discarded his companions as primitives wasn't the same as _this_; his current pursuers would completely cut Amy's timeline to pieces simply for the 'crime' of associating with him; he _had _to leave her once this was dealt with...

But, on the other hand... if she was already dreaming about the Faction... that overly-large house... the lack of information about what happened to her parents... and he'd heard rumours of 'Paradox orphans' in some of his travels; he needed a few more answers, but the facts she'd given him so far _did _tie in to those stories...

Maybe, just maybe, this _once_, he had met someone who would be safer if he stayed than she would be if he left...

As he finally reached the Royal Leadworth- it wasn't the biggest hospital he'd ever been to, but it should have what he needed-, thoughts of what he would do later were pushed aside in favour of what he had to do now as he and Amelia hurried into the main lobby, the Doctor pulling out his psychic paper to show it to the receptionist waiting to greet them.

"Computer maintenance check; _out_," he said firmly as he walked behind the desk, his authoritative manner trumping his raggedy attire as the woman behind the desk obeyed his command.

"What are you doing?" Amelia asked, as he began to rapidly tap away at the computers in front of him; he might not be a Melanie Bush when it came to the fine details of computer programming code in this era, but he had picked up a lot of practise in this technology over the years.

"Well, firstly, I just need to confirm that this is the right place- ah-_hah_!" he said, grinning as he pulled up a picture of a man he recognised from his brief contact earlier in Amelia's house. "Knew it!"

"What?" Amelia asked, walking over to look at the image in confusion. "It's... a patient?"

"It's a _coma _patient whose face I saw in Prisoner Zero's mind when I linked with it," the Doctor clarified, smiling back at her.

"Hold on; you... linked with it?" Amelia said, her eyes wide as she looked at him, her childish natural ability to leap to the obvious conclusion helping her realise what he had done before many adults had in the same situation. "You read its mind?"

"It's only something I can do when I make physical contact, and this isn't the time for that; what _is _important right now is that what I'm reading here proves my theory," the Doctor said, smiling as he indicated the information before them. "Five comas of unidentified cause, all living within the general vicinity of your house; as a multi-form, Prisoner Zero can disguise itself as anything, but it needs a lifefeed- a psychic link, with a living, but _dormant_, mind- so that it can maintain that disguise."

"But... you mean it put these people in comas _in case _it wanted to use their bodies?" Amelia said, her eyes wide in horror and disgust at the implications of what she'd just learned. "I mean, it can't be _all _of them at once..."

"Precisely; it's keeping them just _in case _it needs them," the Doctor said, nodding grimly at her before he reached over to remove a small camera from a nearby drawer, taking a brief break to hook it up to the computer before he turned his attention to more immediate matters.

"Now then," he said, grinning over at Amelia, prior anger at Prisoner Zero forgotten, "first things first; sun's gone wibbly, so right now, somewhere out there, there's gonna be a big old video conference call, all the experts in the world, panicking at once, and d'you know what they need? Me."

Enjoying the slight smile on Amelia's face at that word- it was always nice when he was able to live up to his opinion of himself, particularly these days-, the Doctor grinned as he entered the IP address that UNIT had established for such a crisis- he might not have used it much, but being a time-traveller and near-founder of this organisation had its advantages-, quickly finding himself facing a screen of the very people he needed.

"Ah, here they are, all the big boys!" he said, smiling over at Amelia. "NASA, Jodrell Bank, Tokyo Space Centre, Patrick Moore..."

Giving them a moment to process his presence as he held up the psychic paper, the Doctor smiled casually at the men on the computer screen before he began to tap away at the keyboard. "I know, you should switch me off, but before you do, watch this; Fermat's Theorem, the proof, and I mean the real one, never been seen before, poor Fermat got killed in a duel before he could write it down- my fault; I slept in," he added, glancing over at Amelia awkwardly before he smiled and turned back to the current matter. "Oh, and here's an oldie but a goodie- why electrons have mass-, and a personal favourite of mine; faster-than-light travel with two diagrams and a joke."

As he stopped typing for a moment, he wasn't sure what was more satisfying to him right now; the slightly stunned expression on the face of the geniuses before him, or the enthusiastic smile on Amelia's face as she looked at him.

"Look at your screens," he said, focusing on the immediate priority right now. "Whoever I am, I'm a genius. Look at the sun; you need all the help you can get. Fellas, pay attention."

With that, he opened up another program and began to rapidly type, turning to look over at Amelia even as his fingers flew across the keyboard.

"Amelia," he said, his fingers on automatic as he spoke, "find the coma war- it's on the upper level, apparently- and get every conscious person out of there; use this-", he continued typing one-handed as he used the other to take the psychic paper out of his pocket and hand it to her, "-to convince them; it's slightly psychic, so just focus on showing them something that will persuade them to take orders from you and that _should _be enough."

"But I'm just fourteen-!" Amelia began.

"Which is why you'll need _this_," the Doctor said, pausing to turn away from his work to pull the TVG out of his pocket, giving it a quick once-over with the sonic screwdriver before he handed it to her. "It's not perfect, but its dimension-warping capabilities can be modified into a basic perception filter without too much effort; so long as you don't draw attention to your age, everyone should accept that you _look _old enough to be giving them orders."

For a moment Amelia could only stare at the TVG and the psychic paper, her eyes wide and her mouth hanging slightly open, before she looked back at the Doctor with a smile.

"No one's _ever_..." she said, swallowing slightly as she grinned back at him, before she nodded resolutely at him. "I'll do it."

"I know you will," the Doctor replied, smiling at her before he turned his attention back to the computer in front of him, his fingers flying over the keys as Amy ran for the stairs.

"_Sir_," one of the men on the screen said, after he had remained silently focused on his work for several moments even as the video continued running,"_what are you doing_?"

"I am writing a computer virus, very clever, super fast, and a tiny bit alive, but don't let on," the Doctor said with a smile as he entered the final commands before activating the computer's e-mail. "OK, I'm sending this to all your computers. Get everyone who works for you sending this everywhere. Email, text, radar dish. Whatever you've got, any questions?"

"_What does this virus do_?" one of the men asked.

"Oh, it's a reset command, that's all," the Doctor said casually. "It resets counters; it gets into the transmissions and resets every counter it can find; clocks, calendars, anything with a chip will default at zero at exactly the same time."

As he spoke, a thought occurred to him, and he looked more directly at the screen; if he was going to ask them to broadcast a virus, he was going to need to give them something more. "But yeah, I could be lying, why should you trust me? I'll give you this; I am the Doctor, I have the ear of the UN and Brigadier Alistair Gordon Lethbridge-Stewart, I have saved this world more times than many of you have had hot dinners, and I am _not _going to let this be your end."

The intensity of the stare might have helped, but right now the Doctor wasn't interested in the fine details of why the people on the screen were listening to him after that speech; with approximately twelve minutes to go, all that mattered was that they were.

And... for the first time since that last dark day travelling in Compassion, it felt good- it felt genuinely _good_-to identify himself as the Doctor to the people he was trying to save; he didn't know why, but, after so long saving the day because he was the only one left who really could, it felt like he was saving it with a purpose.

"Right then," he said, smiling as he flexed his fingers over the keyboard, deciding to ponder that personal revelation later, "let's do this, shall we?"

For the next few minutes, the Doctor and the rest of the people on the screen were working on ensuring the spread of the Doctor's virus- this would have been easier a few years in the future when wi-fi- was more available, but the communication facilities available to him in the present weren't exactly to be sneezed at either-, the Doctor making any necessary modifications as the rest of the people on the screen continued to send it off to their relevant companies and contacts, until a red-haired figure hurried down the corridor towards the reception desk with a broad smile.

"Ah, Amelia Pond!" the Doctor said, smiling as his young friend hurried to stand behind the desk and look at him. "All well, I trust?"

"I told them that a private physician needed to take a look at the patients in that ward because we had reason to believe that a rare virus was responsible for their comas," Amelia said with a smile as she handed the psychic paper back to him. "It's not much, but it seemed to get the job done."

"Always best to stick to the facts when you can, Amelia; make your story too complicated and you run the risk of getting caught out," the Doctor said, nodding in approval at her before he turned back to the screen. "Everyone, you've got the virus, so just keep on sending it; I've got to track down the _source _of the problem."

"_Good luck_," someone said at the other end.

"You too, gentlemen," the Doctor replied, nodding briefly at them before he took Amelia's hand once again. "Come along then, Amelia; we've got to get to that ward."

"Uh... any particular reason we're going there?" Amelia asked, even if she displayed no reluctance to obey the Doctor's suggestion as she ran after them.

"Oh, now that Prisoner Zero knows I'm here its main priority will probably be to ensure that I don't do anything to disrupt its disguises so that its jailers can find it; get to the ward where its 'templates' are being kept, and we've got a good chance of finding it," the Doctor explained, smiling at the girl as they hurried up the stairs.

"You... you really think you can stop it?" Amelia asked, looking at him with a slightly uncertain expression as she stopped running, the two of them half-way up the stairs to the next level.

"I scare the Faction, Amelia Pond," the Doctor said, smiling slightly at her with a grim expression as he walked slightly downwards so that his eyes were level with hers. "Do you really think I'd do _that _if they didn't know I could do some damage to them and everything they worship... _including _the loa that Prisoner Zero is one of?"

He didn't know precisely what Amelia knew about the Faction- he knew that they had established some kind of presence on Earth since the temporal split had taken place, but he'd never been able to find anything definite about their role in society; they were essentially a real version of that 'Magnate' that poor, delusional Jeremy had believed was giving him orders without actually _ruling _anybody-, but he hoped that would be enough to convince her that he knew what he was doing.

The Faction might be too widespread for him to defeat them on a large scale right now, but if he could help these jailers deal with Prisoner Zero, maybe it would be a start to proving to the universe- and, more importantly, proving to himself- that he could still fight them...

As he hurried into the coma ward, he allowed himself a brief but satisfied smile at the sight in front of him; an older woman in a blue suit, two little girls about the age Amelia had been when he first met her holding her hands, looking down at an exact mirror image of herself lying in the bed.

"Ah, good, you're already here," he said, smiling as he closed the door behind him and Amelia, giving it a quick blast with the sonic screwdriver behind his back even as he kept staring at the woman who was even now turning to face him; Prisoner Zero could probably get in no matter what they did, but it was good to know he didn't have to worry about that.

"And you... are _here_," the woman who was clearly Prisoner Zero said, turning to look at him with a slightly satisfied smile. "All those years of running-"

"It's not like your worshippers are any more skilled at staying put, so don't get into that," the Doctor said, staring firmly at Prisoner Zero as he manoeuvred himself so that Amelia was just behind him; the last thing he wanted was to draw any more attention to her than he had already, which therefore made it _very _important to keep Prisoner Zero focused on him. "Talking of which, how did you get captured anyway?"

"An impermeable prison for a highly malleable entity," the creature said, shrugging as she/it looked back at the Doctor. "Manifestation is easier these days, but it's not without its handicaps..."

"Manifestation?" Amelia asked, giving the Doctor's hand a slightly questioning squeeze.

"The Faction primarily personifies concepts and paradoxes rather than entities that exist in a sense that you or any human could fully understand," the Doctor said, keeping his voice low even as he kept his gaze fixed on Prisoner Zero; do _nothing _to give the impression that he considered Amelia as anything other than someone in the wrong place at the wrong time, and Prisoner Zero should leave her alone. "Used to be difficult to pull it off, but with reality a bit more malleable than it was in the days before the Fall, things are a bit easier for them..."

"As you would know, wouldn't you... Time Lord?" Prisoner Zero said, sounding somehow satisfied and scornful at the same time as it looked at him.

"You know who I am, then?" he asked, hoping that he could sound more casual than he felt; judging by the brevity of their actual contact so far, he doubted that Prisoner Zero could have had enough time to alert any of the Faction to his location- if it was simple to call for help, it would have left Earth to rejoin them long ago-, but it was best to be sure of his ground before he started any further debates, particularly when it might still take a minute or so for everyone on his 'team' to get the virus dispersed properly...

"We have always known you, Doctor," Prisoner Zero said, smirking slightly as it looked at him. "Do you really think that the Faction would forget you?"

Somehow, the fact that Prisoner Zero confirmed that so casually made the Doctor angrier than ever; even after they'd taken everything else from him, reducing him to a shadow of what he'd been, they _still _wanted more from him.

It was enough.

Subtly sabotaging the Faction's efforts and leaving after he'd defeated them wasn't enough any more; one of their gods had staked a claim on his friend- there was no other reason for Prisoner Zero to have stayed in Amy's house in particular for all these years-, and he was _not _going to let that stand.

"Look, where's the point of all this?" he asked, raising an eyebrow as he tried for a casual smile to conceal his own emotions at the creature's last comment; he might have renewed his to fight, but that didn't mean he wanted this to die. "You take the disguise off, they'll find you in a heartbeat; nobody dies, everyone's happy."

"The Atraxi will kill me this time," Prisoner Zero said, in a childish tone that suggested that it was a mother reminding her son of something he really should have remembered before now. "If I am to die... let there be _fire_."

"Even knowing the scale of the paradox that's going to cause?" the Doctor pointed out, even as a part of him was grimly minded of Lord Sutton's final act; he'd certainly met enough beings in the past who were willing to destroy the world if they couldn't rule it for themselves. "We both know there's only so much the Faction can do even now without destroying themselves-"

"But _we _are not doing this, Doctor," Prisoner Zero replied, the two girls shrugging along with their 'mother' as they smiled nonchalantly at him. "I have created the reason for this attack, but my followers are not mounting it; the Atraxi are the ones responsible, not us."

"Yeah, but removing humanity from the equation eliminates the potential for all kinds of juicier paradoxes in the future," the Doctor countered, trying to catch his enemy out with a decent argument for leaving. "Look, you came to this world by opening a crack in space and time; why not do it again and leave?"

"I did not open the crack," Prisoner Zero replied.

"You didn't?" the Doctor said, curious despite himself; he'd known that the loa weren't as powerful as the Faction and others liked to pretend/imagine they were- even in a world where belief and concept played a greater role in shaping reality than it had before without the Time Lords to enforce the rules, belief could only take you so far-, but to hear one admit that it couldn't do something raised some interesting questions. "Well, _somebody _did; if not you, than who?"

"The cracks in the skin of the universe..." Prisoner Zero said, chuckling slightly as she/it looked at him. "You don't know where they came from?"

"The Doctor in the TARDIS doesn't know," a little girl's voice suddenly said, sounding very pleased with itself about this new information as she continued speaking in a singsong manner. "Doesn't know! Doesn't know! Doesn't know!"

"The universe shall crack," Prisoner Zero continued, now returned to the mother's voice. "The Grandfather's Prophecy shall be fulfilled when the Pandorica opens."

For a moment, the Doctor thought about asking what the creature meant by that, but then his gaze fell on the clock behind it and thoughts of the 'Pandorica' were pushed aside (He'd worry about that later; with everything else the Faction had on their side, one more fairly tale was nothing to be that concerned about).

"Aaand we're off," he said, grinning as he raised a hand to point behind Prisoner Zero. "Look at that."

As Prisoner Zero glanced in the direction that he'd just pointed, the Doctor didn't need to see its expression to know that it was confused; the sight of a clock suddenly shifting to zero was confusing, but it wasn't that strange.

"Yeah, I know, just a clock, but d'you know what's happening right now?" the Doctor asked, smiling casually at Prisoner Zero. "Right now, across the world, my team are working away, spreading the word from satellite to screen to counter, as fast as modern technology will allow- they've probably got this hemisphere already and they're definitely spreading out further-, and y'know what the word is? The word is zero."

For the moment, Prisoner Zero was merely looking sceptically at him, but the Doctor could almost _feel _Amy's pride radiating from behind him, and that was more than he needed right now; Prisoner Zero's reaction was coming soon.

"Now, me," he continued nonchalantly, "if I was up in the sky in a battleship, monitoring all Earth communications, I'd probably take that as a hint. And if I had a whole battlefleet surrounding the planet, I'd be able to track a simple old computer virus to its source in... what, under a minute? The source, by the way... is the computers in this hospital; bit slow, but they did what I needed them to do."

No sooner had the words passed his lips than a light filled the window outside the hospital, prompting the Doctor to smile. "Ah, there we go; they found us!"

"The Atraxi are limited," Prisoner Zero said, shaking her/its head as she looked at him. "While I'm in this form, they'll still be unable to detect me. They've tracked a computer; not me."

"Yeah, but this is the best bit- the _really _good bit-; those computers include information on all five of your comatose victims that you're using for a disguise," the Doctor clarified, smirking at her. "They might not be able to tell you apart from humans right now, but I'm _pretty _sure there's enough information available for them to realise what the human norm is, and therefore give them all they need to realise that the only reason these patients are the way they are is _you_; you're not exactly going to be able to claim mistaken identity _now_, and with these doors locked the only way out is for you to return to your natural form, which will result in you being pretty much done for anyway if I'm understanding your plight correctly."

"So... it's stuck?" Amelia's voice asked, looking at the Doctor with a smile on her face when he glanced back at her.

"Completely," the Doctor said, nodding in confirmation at Amelia before he turned back to Prisoner Zero. "So, the final score; no TARDIS, minimal use of the sonic screwdriver, contemporary technology only, four minutes to spare; _who da man_?"

The silence that greeted that statement was all the confirmation he needed that he'd just said the wrong thing.

"I'm _never _saying that again..." he muttered in frustration.

"Then I shall take a new form," Prisoner Zero said smugly.

"Oh, stop it; we all _know _you can't," the Doctor said, looking back at Prisoner Zero with a slight smile of amusement; it was kind of nice to deal with an enemy that tried to bluff when he _knew _it had nothing. "It takes _months _to form that kind of psychic link-"

"And I've had seven years," Prisoner Zero said, beginning to glow just as the Doctor heard Amelia fall to the ground behind him.

"_NO_!" he yelled, spinning around to crouch down beside the young girl, placing his hands on her face as a quick glance confirmed that she was at least still breathing whatever else happened to her. "Amelia, hold on! Wake up! _Amelia_!"

The sound of something slithering- that was the best term he could use for the sound he was hearing- into itself caused him to glance up, only to be briefly confused at the sight of the man before him with a near-rectangular face and floppy brown hair before he took in the other man's attire of a torn blue shirt and brown trousers and realised what he was looking at.

"You're _me_?" he said, laying Amelia down on the floor as comfortably as possible and walking over to confront the alien. "But... why me? You're linked to _her_; why are you copying me?"

"I'm not," another, smaller voice said, something apparently emerging from the other Doctor's back to reveal the child-form of the Amelia Pond he'd met barely two hours ago in his timeline and seven years ago as far as the rest of history was concerned, looking up at him with a scornful smile.

"Poor Amelia Pond," the little girl said, looking at the body of what could have been argued to be her older self. "Still such a child inside. Unaware of the monsters in her house, preparing her dreams even as she herself dreams of the magic Doctor she knows will return to save her..."

Looking him over, the child-Amelia/Prisoner Zero shook her head slightly in mock scorn. "What a disappointment you've been."

_Child inside_...

'There's no point in being grown-up if you can't be childish sometimes'; he'd said that once, lives and years ago, but even being childish sometimes didn't change the fact that you had to grow up.

Had he prevented her from...?

_No_.

He'd made a mistake, but Amelia Pond still had a chance to grow beyond the girl who'd waited for him all this, and he was _not _going to let this _thing _destroy that chance just because Prisoner Zero would rather die in a blaze of paradox-causing glory than accept defeat.

He didn't know enough about this thing to feel comfortable using the sonic screwdriver to try and disorientate it into returning to its original form without triggering a feedback loop that could harm Amelia in the process, and his mind might be sharp right now but he _knew _he wasn't stable enough to try and link with something like this to force it into the shape he wanted...

As soon as the idea had occurred to him, the Doctor had hurried over to crouch down beside Amelia, her small form- albeit larger than it had been- in front of him as he placed his hands on either side of her head.

"Amelia," he said, his gaze fixed on her, ignoring Prisoner Zero- anything it tried to do in order to interfere with his current actions would only draw attention to itself- as he addressed the young girl, focusing his own thoughts on his words, "don't just hear me, _listen_. Remember the room, the room in your house you couldn't see. Remember you went inside, I told you not to but you did. You went in the room. You went inside. Amy... dream about what you saw."

For a moment, as he brushed across her mind with his still-reforming psychic senses, he allowed himself to enjoy the feeling of her faith in him- a strong, almost golden, warmth that enveloped his presence in her mind as though welcoming him back into her life, a faith that could not be shaken no matter what she had endured while waiting for him-, and then he focused on the image she'd seen when entering the forgotten room, the image of him facing Prisoner Zero, the image of Prisoner Zero ready to attack them both in its natural serpentine form...

Glancing back as he heard a scream of defiance and rage, the Doctor smiled and stood up as Prisoner Zero reverted from its appearance of him and young-Amelia to its tailless snake-form, staring angrily at him.

"Oh, well done, Prisoner Zero," the Doctor said, smiling at his enemy. "A perfect imitation of yourself."

Before Prisoner Zero could do anything to respond to his taunt, light shown through the window, leaving Prisoner Zero twisting and screaming in rage as

"_Prisoner Zero is located_," the voice of its jailers- the beings the prisoner in question had identified as the Atraxi- said. "_Prisoner Zero is restrained_."

As the Doctor watched, Prisoner Zero vanished into the air as the glow faded, its appearance turning transparent even as he watched, leaving the Doctor to stare grimly back at it even as his mind reverberated with the creature's last words.

_He will find you, Doctor_...

From anyone else, it might have been an empty threat, but this wasn't just anyone; he knew the Faction better than any man outside of their order, and these days, they didn't _make _empty threats.

If _he _found him...

_No_.

Whatever happened next, the Doctor would _not _allow the Faction to find the now-stirring Amelia Pond.

But first, as the sunlight returned to normal, he had a more immediate situation to deal with...


	5. Facing the Atraxi

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

The History of Paradox

As Amy stirred back into consciousness, she was momentarily surprised to find herself looking at the Doctor standing over her, smiling warmly down at her, before her memory caught up with reality; recent events _hadn't _been a dream and the Doctor was _really _back in her life...

For a moment, horror dominated her mind as she looked in the direction where Prisoner Zero had been standing earlier, but she relaxed when she took in the creature's absence; judging by the Doctor's own lack of concern, it seemed like a good assumption that the thing that had lived in her house for all those years was now gone.

"It's... it's over?" she asked, looking anxiously at the Doctor as she slowly sat up. Checking herself over in case anything was missing, she was relieved to feel the slight bulk of the TVG in her inner jacket pocket; it was a bit uncomfortable against her chest, but at least she didn't have to worry about it falling out without her noticing its absence.

"Prisoner Zero's dealt with, but I'll need to get back to you on the other bit; just give me a moment..." the Doctor said, pulling a small phone out of his pocket and pointing his 'time wand'- Amy wished she knew what that thing was called- at it as he continued speaking. "Just need to track the signal back... got it!"

Before Amy could ask what he meant by that, he had raised the phone to his ear and begun to speak. "Oi; I didn't say you could go! Under Article 57 of the Shadow Proclamation, _this_ is a fully established level five planet, and you were gonna burn it? What; did you think no one was watching? You lot. Back here, now."

With that, he terminated the phone call, looking grimly back at Amy as he tossed the phone to her, Amy only just able to catch it as she processed what she'd just heard.

"_Now _I'm done," he said, his expression grim as he walked towards the door of the ward.

"Uh... did you just call the aliens _back_?" Amy asked, looking at her friend in shock before she got to her feet and began to hurry after him. "Where are you going?"

"The roof!" the Doctor proclaimed as he walked down the corridor, only to suddenly change direction and walk through another door. "No, wait..."

As she hurried into the room after him, Amy was surprised to find that they'd detoured into a changing room, with the Doctor already pulling shirts out of the open lockers and studying then.

"What are you doing?" she asked in confusion.

"I'm saving the world; I _need _a decent shirt," the Doctor said, tossing a couple of shirts away as he continued walking down the corridor. "To _Hell_ with the rrrraggedy! Time to put on a show!"

For a moment, Amy felt like letting out a little chuckle at the Doctor's mock-Scottish accent- it sounded a little like something he'd heard a while ago and couldn't imitate correctly-, but then she realised that the Doctor was already taking his shirt off and tossing his tie away and turned around as quickly as possible; she might like the Doctor, but she was _not _going to watch..._that_...

"Uh... do you have to... well, you're just going to... _take _those?" she asked, trying to think of something _other _than the fact that the man she'd dreamed about since she was a little girl was currently stripping right behind her.

"Well, I'll look into getting them back once I've found the equivalent in the TARDIS wardrobe- you can find anything in there if you just spend the time looking, regardless of taste; you don't want to know _what _I was wearing regularly a few centuries ago-, but right now, I think that the need to be properly dressed when saving the world takes precedent, wouldn't you?" the Doctor said, sounding very satisfied as she felt something hit the back of her foot; glancing down, Amy noted that it was one of his shoes, but still didn't dare to turn around and look just yet. "Anyway, still a couple of things I need to decide on... well, that should be fine."

Glancing back for a moment, Amy relaxed when she noticed the Doctor doing up the buttons on a reddish-pink shirt, his legs now covered by dark trousers and shoes with what looked like suspenders hanging down around his sides and a series of ties draped around his shoulders.

"Come along, Pond," the Doctor said, grinning at her as grabbed a couple of jackets from some more lockers and tossed them over to her. "They should be here soon, and it's rude to keep your guests waiting; best to answer their questions now rather than later."

"Uh... OK..." Amy sad, stuck for anything else that she could say or do as she hurried after the Doctor as he resumed his walk towards the roof, heading up another flight of stairs to emerge on the roof of the Royal Leadworth. Glancing upwards, Amy tried not to yell at the sight of the eye that she'd seen through the crack all those years ago staring down at them from within what looked like an elaborate crystal circle, with multiple sharp points coming out of it, some kind of blue energy crackling around the eye in the middle and the points glowing as it hovered in position.

"So... this was a good idea?" she asked uncertainly. "They were leaving... weren't they?"

"Leaving is good, but never coming back is better; you've all got enough problems without any more trying to make Earth their concern," the Doctor said, before he called up to the ship floating above them with a casual stance that belied the intensity of his earlier words. "Come on! _The Doctor will see you now_!"

As though responding to the Doctor's call, the eye in the centre of the ship suddenly zoomed down to hover in front of him, Amy taking a couple of anxious steps back as a blue light flared out from the centre of the eye to scan over the Doctor before retreating back into its 'iris', even as the eye itself continued to hover in front of them.

"YOU ARE NOT OF THIS WORLD," the eye said, its voice surprisingly deep for something that shouldn't even have vocal chords.

"No, but I've put a lot of work into it," the Doctor replied, pulling his braces up over his shoulders before he turned his attention to studying the ties around his neck, muttering thoughtfully to himself before he held one of them up as though seeking the large eye's opinion. "What do you think?"

"IS THIS WORLD IMPORTANT?" the eye asked.

"Important?" the Doctor asked, tossing one tie over his shoulder to land on Amy. "What does that mean, important? Six billion people live here; is that important?"

As he spoke, he tossed the rest of his temporary ties over his shoulder, leaving Amy with ties draped over her arms and the jackets she was carrying as she stared uncertainly at the sight before them.

"Here's a better question," the Doctor continued, staring intently at the eye before him, "is this world a threat to the Atraxi?"

There was a moment's silence as the Atraxi appeared to consider the Doctor's question, until he spoke again. "Come on, you're monitoring the whole planet; is this world a threat?"

As though in response, the eye projected a large blue globe, flicking through various images of armies and explosions before being contrasted with a few images of what looked like religious figures; Amy was fairly sure she caught a glimpse of Ghandi in there...

"NO," the creature said, as the image ceased.

"Are the peoples of this world guilty of any crime by the laws of the Atraxi?" the Doctor continued, as he reached up to do up the last of his shirt buttons.

"NO," the eye said again, after another series of images were displayed, these ones showing what looked more like people going through their daily lives; Amy even saw someone apparently dancing or jumping.

"OK," the Doctor said, reaching into his pocket to pull something small out of it, adjusting his collar as he continued to address the eye. "One more, just one... is this world protected?"

As Amy watched, the eye's projection changed to show various unfamiliar but clearly alien images; something that looked like robots, a figure that put Amy in mind of a pepperpot with a plunger, a gun and an eye on a stick, a creature with an oval-shaped head with what looked like octopus suckers around it, smooth-skinned men that almost looked like plastic, a short alien with a dome-like head in some kind of armour, reptiles with a third eye on the top of their heads, a creature with a woman's upper torso and a spider's legs and main body, giant furry things that made her think of old tales she'd heard of the Yeti...

"'Cause you're not the first ones to have come here; oh, there have been _so _many," the Doctor said, tying what Amy now bizarrely realised was a bow tie around his neck- she'd spent so long remembering him as the Raggedy Doctor with his long brown tie that it was strange to imagine him with something that small- as he continued to address the eye amid its latest slideshow. "So what you've got to ask is... what happened to them?"

As he walked back to Amy, taking a tweed jacket out of her arms, Amy could only stare at the images now being projected in front of the eye; an old man with grey hair and a hawk-like nose in a Victorian-esque suit, a shorter man with a weathered face and a haircut that reminded Amy of classical monks in a baggier version of the last man's clothes, an older man with slightly curly white hair in an outfit that bizarrely reminded Amy of Austin Powers, a man about the same age with thick curly brown hair in a long scarf, a younger man with short, straight hair in a long coat with what looked like a sick of celery on his lapel, a man with fairer curly hair in a patchwork-looking coat, a short man in a straw hat carrying an umbrella, a taller man with curly hair dressed in an Edwardian outfit, a man with close-cut hair in a leather jacket, a thin man in a brown suit and a long brown coat...

"Hello," the Doctor said, walking through the last image as it shut down, revealing his new attire of a tweed jacket, red bow tie, pale reddish-pinkish shirt, and dark trousers, "I'm the Doctor."

For a moment, he stood there, his whole body conveying a sense of satisfaction in those last words as he stared at the large eye before him, Amy unable to stop herself from smiling at the sight, until the Doctor spoke again.

"Basically..." he said, a slight chuckle in his tone as he spoke. "Run."

As much as a bodyless eye could be said to have widened in shock, the eye in front of them did just that, retreating back to the crystal ship above it before the ship itself began spinning around rapidly before it hurtled back towards the sky, leaving the two of them standing on the rooftop, looking up after it with varying smiles.

"So... that's it?" Amy asked at last as the ship vanished from view, looking curiously at the Doctor. "They're gone?"

"Unless something else from that prison of theirs escapes here, and I find that unlikely; it's a big universe with plenty of other places to escape to, after all," the Doctor said, smiling as he looked back at her, a thoughtful expression on his face for a moment as he looked at her before he smiled, as though he'd just come to a decision, and continued speaking. "Anyway, at least that's that sorted out; the loa's dead, the Atraxi aren't coming back, and the TARDIS should be coming along nicely; only thing left to do is for me to work out where I can stay here-"

"Hold on; _stay_?" Amy repeated, her eyes widening incredulously as she looked at the Doctor in shock, barely able to believe that she'd just heard him say that word; after he'd left her so abruptly last time, the idea of him _not _leaving seemed almost as strange as the idea of him asking her to leave with him. "As in, you're staying _here_?"

"Well... no offence, but you're not quite old enough to be running around time and space with me as you are- basic rule of time-travel I established after a couple of past close calls; you need to have at least left school before you do anything else-, and I'm not leaving you to wait even _longer_ after all that, so the best compromise is for me to stick around and keep an eye on things until you _are _old enough," the Doctor said, shrugging slightly as he looked back at Amy, as though he wasn't confirming every hope and dream she'd had since she was seven. "Should be safe enough so long as I'm careful-"

The Doctor's further words were cut short as Amy practically leapt onto him, wrapping her arms around him and grinning broadly as she rapidly yelled out her gratitude.

"Thankyouthankyouthankyou!" she said, grinning up at the Doctor with such a broad smile she felt like the top of her head was going to fall off.

"No problem," the Doctor said, smiling back at her as he gently disentangled her arms from around him. "Just give me a day or two to sort out a few small things, and I'll be right back, I promise."

Noting the suddenly sceptical expression on his face- as much as Amy wanted to trust him, she couldn't forget what had happened the last time the Doctor had promised something like that-, the Doctor smiled reassuringly at her. "Could you just give me the TVG for a moment?"

Looking uncertainly at him, Amy nevertheless reached into her jacket to pull out the stick-like object in question, the Doctor briefly aiming his silver thing at it before handing it back to her with a smile.

"Just dialled up the TARDIS's perception filter by remote; we'll still know it's there, but everyone else won't be able to register it as anything more than something they don't want to see," the Doctor said, shrugging slightly as he watched her slip it into her pocket. "Just keep it safe- and don't go into the TARDIS with it; I'm not sure what would happen if it was inserted back into the old girl while she's still trying to repair herself-; I'll be back for it soon, I promise."

As the Doctor turned to hurry down the stairs, Amy could only stare after him for a moment before she took the TVG out of her pocket and stared at it, a broad smile on her face at this new proof.

The Doctor was _real_...

He'd saved the world...

He'd defeated Prisoner Zero...

And he was going to _stay_?

Amy didn't think she'd ever had a better day than this.

If only she could explain that strange... _feeling _she got when she received one of the Doctor's smiles; she'd always known that he wasn't like anyone she'd ever met, but she definitely didn't remember feeling like _that _when he looked at her when she was younger...

* * *

><p>AN: Hope you enjoyed that; coming up in the next chapter, the Doctor will visit two old friends, one that anyone familiar with the classic series will recognise near-instantly, and another from the Eighth Doctor novels whose history with the Doctor in this world was <em>very <em>different...


	6. Building a Life with Old Friends

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: For reference, I'm assuming that the country house the Doctor visits here is somewhere near London, but otherwise I feel comfortable being relatively lax about specific travel time given the vehicle he'll be acquiring here...

AN 2: Some vague spoilers for the Eighth Doctor novel 'Escape Velocity' here, but there's enough differences from the original plot that it shouldn't significantly spoil it for anyone who hasn't read the story already

The History of Paradox

As he drove away from Leadworth after a quick glance at the map in the car he'd borrowed- he'd see about returning these things once he'd attended to his next stop; he was just glad that he didn't have to drive for more than a couple of hours to get where he was going-, the Doctor couldn't stop himself from wondering about his latest decision during the hours of driving that followed; after so long alone, was this _really _the time to take on a new companion?

He knew that he owed Amelia Pond something for keeping her waiting, and he couldn't deny that he'd been lonely travelling along for so long- his brief time travelling with Jack had been nice, even if the aftermath had left him even more metaphorically 'gun-shy' than he had been-, but at the same time, she was still so young compared to so many of his past companions- Dodo was the only person who'd travelled in the TARDIS at that kind of age in the past (Sam had been young, but she was still old enough to have at least potentially left school if she'd wanted to do so), and if what had happened to her wasn't a clear example of why he shouldn't take children in the TARDIS he didn't know what did-; wouldn't it make more sense to leave her to adjust to the real world before he permanently affected her future ability to cope without him?

But... in the end, he knew he couldn't do that.

Not only had he already drawn the Faction's attention to her in a manner that he knew would leave them more determined to claim her for their own, there were too many things about her life that just didn't make sense.

The crack aside, her house was far too large for just her and her aunt to be living in, and then there was all that stuff she'd said about her having dreams about the Faction's presence, to say nothing of that... _gap _he'd felt when he'd been linking with her to 'nudge' her dream about Prisoner Zero; it was as though certain parts of her life- both older ones, with gaps stretching back to before he'd ever met her, and something that had only gone missing in the last few days or so at most- had been completely erased from history for some reason.

_Something _about Amelia Pond didn't fit, and he couldn't take the chance that she'd suffer because of it; he might or might not be able to help her make sense of the anomalies if he stayed, but he knew for a fact that she'd never find the answers without him.

Still, if he was going to take on a new companion- regardless of his motives for choosing her rather than anyone else-, he was going to do it properly, and that included making sure that Amelia Pond had as thorough an education in what to expect when she got out there as he could; part of the mistakes he'd made in the past was that he'd allowed people into the TARDIS on relatively limited 'excuses'- save for those occasions when circumstances forced him to take off and his current ability to control the ship didn't allow him to take them back more promptly- and they'd just kept on getting into varying degrees of danger because they'd had no idea what to expect...

He wasn't going to do that again; before Amelia Pond went _anywhere _that could he considered dangerous, he was going to make sure that she knew enough to cope with some of the more obvious threats that she might encounter with him. He could probably include a trip or two a year to 'whet her appetite' so long as he took care to establish that the times they were visiting were safe- maybe a visit to a few old friends could be an idea; he hadn't seen some of them for a while apart from his last pre-regenerative 'visits', and observations from afar to remind himself of the way things had been weren't the same as actually having conversations with them-, but for the moment she'd have to be content with a few lessons; if he could manage to help Jo improve her science skills during his time at UNIT when he was also working on repairing the TARDIS and directly working to protect Earth into the bargain, he had little doubt that he could teach Amy what she needed to know if he was primarily devoting his time to that purpose.

He'd probably need to refine his plan for what he'd teach her and when he'd teach her certain things later, but what he had so far should be enough for the immediate purpose; he'd worry about the finer details when he had to, and to get to that stage, he'd need to sort out the business that awaited him at the end of this drive...

* * *

><p>A couple of hours after leaving Leadworth, the Doctor parked his car outside the house that had been his destination, smiling in satisfaction at the sight. He might not travel the conventional way that often, but at least his sense of direction wasn't an issue; over four lifetimes since he'd last visited this place by any route, and he <em>still <em>knew exactly where it was.

He just hoped that the owner of the house wouldn't mind him dropping in like this; the man might be his oldest friend, but he still worried about what might happen if he ever did something to push his former boss too far, and stealing a car to get here might be one of those things...

Pushing his concern aside, the Doctor rang the doorbell, experimentally adjusting his stance- generally the new body felt comfortable so far, but everything needed a bit of 'wearing-in'- until the door opened to reveal a slightly overweight man in his mid-seventies with a white beard, a relatively full head of equally white hair, and an intense stare that no amount of time retired could eliminate.

"Doctor?" the old man said, looking him over with a slight smile. "This is an unexpected visit."

"Always good to see you, Alistair," the Doctor said, smiling back at his oldest human- not meaning to sound racist, but Jack's status as a 'fact' gave him a slight advantage regarding how long he could stay alive for, and in any case the Brigadier had known more of him anyway- friend. "What gave me away?"

"Apart from anything else, only you would go around dressed like that at this apparent age," the Brigadier said, indicating the Doctor's clothes and face with a brief wave of his hand.

"Hey; bow ties are cool," the Doctor countered, adjusting his own as he spoke; it might seem strange, but he rather liked that particular part of his new wardrobe.

"So, what brings you here, Doctor?" the Brigadier asked, ignoring that last statement as he stepped aside to allow his friend inside the house, glancing briefly at the car the Doctor had driven here before he shut the door. "And where's the TARDIS?"

"It took a bit of damage during my last regeneration; I've left her with a friend to repair herself while I... attend to a few things," the Doctor said, smiling slightly awkwardly at the Brigadier.

"Such as?" the Brigadier asked, looking curiously at his friend.

"Well... basically, I need some paperwork drawn up for a new identity, and was wondering if you could get some of the old guard at UNIT to help me set things up," the Doctor replied, shrugging slightly as he explained things to the only man he could ever feel comfortable regarding as his 'boss'; Alistair might be a friend first, but even before Gallifrey's destruction he was the only person the Doctor would have ever felt comfortable taking orders from.

"A new identity?" the Brigadier repeated, looking at the Doctor in surprise. "Is the TARDIS-?"

"Oh, she's fine, really- shouldn't take more than a day or two to get things back to normal-; it's just... well, I made a few promises that I need to stay here to keep, so I'd appreciate the necessary paperwork be drawn up in case I attract too many questions," the Doctor said, smiling reassuringly at his old friend (He knew that the Master had mastered the ability to do this kind of thing himself, but he'd never installed those features in the TARDIS and he wasn't about to start now; relying too much on yourself could be just as dangerous as relying too much on others in a world like this one). "I can give you the general details of where I'm staying and what I need, I can handle the financial side of things well enough, and of course you can consider me available if something comes up that needs my expertise- just don't bother me about the Auton invasion in a couple of years; I've already attended to that two lives ago-, and all should be fine."

For a moment the Brigadier simply sat in silence, looking at the Doctor with a contemplative expression on his face, until he finally smiled in understanding at the seemingly younger man.

"It must be a very special person for you to go to these kind of lengths for her, Doctor," he said.

"When did I-?" the Doctor asked.

"Only a woman could bring out that kind of protective instinct in you, Doctor," the Brigaider said with a slight smile. "And even then only the younger ones; you were always a lot more protective over Miss Waterfield or Miss Grant than you were with Miss Herriot or Doctor Shaw, after all."

"True," the Doctor said, nodding at his old friend with a brief smile before he looked more curiously at him. "So... that paperwork?"

"Just give me a few more specific details about what you're looking for and I'll have UNIT draw something up fairly quickly," the Brigadier said, nodding reassuringly at his friend as he sat down on a nearby chair. "Anything else?"

"Just one thing before we get down to business," the Doctor said, looking hopefully at his friend as he sat down in another chair. "I don't suppose you still have the old girl somewhere nearby, would you?"

* * *

><p>A few hours later, as he stood outside the London office building where his current contact could be found, the Doctor spared a moment to wonder if he had the right to do this.<p>

It wasn't like it was actually creating a paradox- he didn't _know _how her career would turn out given that this wasn't the kind of industry where you attracted major headlines, and he trusted her to be careful enough not to do anything that would attract too much attention to herself-, but it was still hovering on the edge of a line that the Faction crossed on a regular basis; even with the virus erased, it wasn't something he wanted to consider in detail...

But, at the same time, it wasn't like he was going to make a regular thing of this, was it? He was just going to give her a few tips- enough to help her while trusting her judgement to help him in return- and leave it at that; he wasn't changing anything, he wasn't giving her detailed knowledge, and he was definitely _not _going to help her if she decided to use this knowledge to significantly help others outside of her current role.

It was a greyer area than he liked, but it was small enough that the Faction shouldn't notice it was happening...

Taking a deep, resolute breath, the Doctor walked through the doors of the office and headed to the desk in front of him; in a strange way, it was almost unnerving knowing that he probably _wouldn't _have to lie about who he was to get an appointment here.

"Hello," he said, smiling casually at the woman behind the desk. "I need to speak with Anji Kapoor."

"Do you have an appointment?" the receptionist asked, looking inquiringly back at him.

"Not really, but I'm sure she can spare a few minutes," the Doctor replied, smiling back at her. "Just tell her it's the Doctor from Brussels; she'll know what I mean."

As the woman picked up the phone, the Doctor stepped back and glanced briefly at the walls around him; the office was a bit small by his standards, but he supposed that it would be fine if you liked this sort of thing...

"She'll meet you in the conference room, Doctor," the woman said, putting the phone down and smiling at him as he turned back to look at her. "It's just through that door and at the end of the corridor; you'll have it for a couple of hours."

"Thanks," the Doctor said, smiling back at her before he followed the directions, quickly taking a seat at the furthest end of the table from the door; he wanted to give Anji a chance to shut the door before she saw him, just in case she automatically left in the belief that he was lying. After a few moments of waiting, an Asian woman in a professional dark suit jacket and skirt walked into the conference room, closing the door behind her before turning to look at him.

"Hello, Anji Kapoor," the Doctor said, smiling at the woman at the other end of the table as her initial smile faltered. "How's things?"

"Doctor?" Anji said, looking at him in confusion for a moment before she stared more firmly at him, evidently assuming that this was a joke of some kind. "But... I'm sorry, I thought you were-"

"I _am _him, Anji," the Doctor replied, smiling warmly at her. "I've changed a bit since then- actually, I've changed _three _times since then; it's a bit of a complicated story-, but it's me; the man who helped you and Dave save Earth from the Kulan back in 2001, remember?"

He acknowledged that their last meeting had probably meant more to him than it had to Anji- after everything was over she'd just gone back to her own life, after all-, but it would have still been a memorable occurrence for her due to her encounter with aliens.

When he'd met Anji, he'd still been reeling from the destruction of Gallifrey and the simultaneous loss of Romana, Fitz and Compassion; his interest in the news report about the two-hearted man that Dave and Anji had encountered had mainly been prompted by the hope that it would be another Time Lord, but even after learning that the other man was anything but, the implications of the mysterious package in Dave's pocket and the anomaly of the man being on Earth in the first place had been enough to inspire his further interest. The subsequent discovery of the Kulan's presence had been an interesting twist even if he'd been easily able to identify their technology once he examined the package- there weren't that many races with two hearts who used that kind of biotechnology in this part of space-, and, having programmed both of the Kulan-Earth hybrid ships to shut down by trapping them in a compatibility-based feedback loop, it had been fairly simply to take Sa'Motta up to the fleet and convince them to call off the invasion, even if getting the other trapped Kulan off Earth had been a bit difficult; the TARDIS had been so disorientated by its recent rapid recharge that he'd had to disable the temporal circuits to be sure of getting where he wanted to do...

If the universe had been kinder, he might have even asked Anji to travel with him, but while she and Dave had helped to remind him that he could have friends, it had been too soon after Fitz and Compassion had been lost for him to feel comfortable asking anyone to come along with him even if there hadn't been the Faction to consider.

Still, she'd been a comfort and a crucial catalyst to him at a difficult time in his life, and he liked to think that he'd helped her and Dave get along- learning that some of things Dave was interested in were real had definitely helped Anji's opinion of the sci-fi buff-; he could only hope that she'd accept this reunion relatively comfortably.

"But... _how_?" Anji asked, looking at him in shock. "I mean... what is this? Space-age plastic surgery? Did you... body-hop or something?"

"More of the first than the second, really; I can change my appearance when I'm fatally injured, and I had a nasty experience involving a radiation overdose a few days ago- by my perspective, anyway- that necessitated me assuming this appearance," the Doctor said, shrugging dismissively before he looked more seriously at her. "It _is _me, Anji, I promise; everything you and Dave experienced with Sa'Motta, Arthur Tyler, Pierre Yves-Dudoin and Fray'kon happened to me as well."

For a moment, Anji could only stare at him in obvious scepticism, until she finally shook her head with a resigned smile.

"Well," she said at last, looking contemplatively at him, "if a stockbroker can save the world with a time-travelling alien, I suppose making that alien a shape-shifter's not that much of a stretch."

"Nothing wrong with your profession, Anji; I used to save the world with a couple of schoolteachers," the Doctor replied with a smile. "And actually, I'm not a _complete _shapeshifter; I don't change my appearance on a regular basis-"

"OK, gotcha; let's... not focus on that, could we?" Anji asked, looking slightly uncertainly at him- evidently there was only so much she'd be willing to take- before she sat down opposite the Doctor. "So... what's up?"

"I need your help, but before we do that, I have a little something for you," the Doctor said, pulling a recently-purchased newspaper out of his pocket and handing it to Anji, indicating the stock market page. "The stocks I've asterisked are those that, off the top of my head, will do well in the next few years; give me a few weeks and I can provide you with Financial Times issues from the same time period, which you can feel free to use or decline as you see fit."

"Uh..." Anji said, looking uncertainly at the paper that was now in her hands before looking back at him, clearly stunned at the implication of what he was offering her. "Can... I mean, I'm grateful, but..."

"Why am I doing this?" the Doctor finished for her, smiling back at her; he might not want to give her too much detail in case the worst happened, but that didn't mean he had to lie to her either. "Simply put, I'm going to be on Earth for a while- a few promises I've made to a few friends, you know-, and that means I'm going to need a means of supporting myself; I've got some money in a bank that's collected a fair amount of compound interest, but I'd rather have some alternative financial arrangements made in a situation like this so that I don't look like a completely idle layabout, and I trust you not to give me away as your source. All I ask in return is that you help me set up a few investment accounts that will allow me to support myself while I'm staying here in a plausible manner; that aside, you don't have to have any contact with me if you don't want to."

"Doctor..." Anji said, her eyes wide as she studied the papers in her hands. "This... this is... I mean, if you're being serious..."

"I joke around a bit, but when it comes to my friends, I don't mess with their careers," the Doctor said, nodding reassuringly at Anji. "This isn't even a case of 'you scratch my back and I'll scratch yours', as the saying goes; you can do what you want with that information, but if you can give me some help in the process, I'd appreciate it."

"Well," Anji said, smiling slightly back at him after a moment of silence as she took a last look over the marked newspaper, "if you're giving me something like this, I suppose I can set up a couple of additional accounts for you..."

"Thanks," the Doctor said, smiling back at her. "I probably won't need to dip into them that much- I've got some money of my own in a couple of good banks-, but anything to help my current cover is a good thing, really."

"Cover?" Anji repeated, looking at him in confusion.

"Long story," the Doctor said, looking reassuringly at her. "Trust me, you're better off not knowing more."

For a moment, the Doctor worried that the slightly sceptical expression Anji gave him meant that she wouldn't go along with the plan, but the subsequent smile and nod of acceptance that she gave him was all that he needed.

He might not be able to give her the full details of his reasons for making such a request, but Anji Kapoor was going to help him establish the additional background information he needed to establish his background while he remained here to train Amelia; everything else could be handled as it came up.

The first priority after the money was transferred over, of course, was finding appropriate accommodations...


	7. Of Bessie, Bacon, and Changing History

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: This takes place a day or so after the last chapter- even with the Brigadier's contacts, it still took a while for the Doctor to make the kind of arrangements he needs to make here-, and returns to Amy and Leadworth; hope you like it

The History of Paradox

As she stared at the seemingly-invisible police box still sitting in her back garden without anyone else noticing it, Amy couldn't help but wonder if she was just being played for a fool once again.

She might have accepted the Doctor's initial explanation that he'd simply made a few driving mistakes to account for his delay in coming back, but that didn't mean that he'd been totally honest; she hadn't exactly given him much reason to avoid talking to her after she'd caught him outside her house.

OK, the fact that he'd been talking about Prisoner Zero that urgently when he came out lent _some _credibility to his explanation, but given what it had turned out to be and his obvious issues with the Faction, it was possible that he'd just learned what was really there and decided to come back because he'd forgotten about it earlier; in the grand scheme of things, it wasn't like she mattered that much.

Maybe she should just forget everything and move on; Rory Williams had invited her to check out the films showing at the new local cinema that night- it was small, but it could be fairly comfortable if the film was right-, but she'd wanted to stick around in case the Doctor came back for his box...

The box.

That was the one thing that always stopped her from convincing herself to give up; nobody would just abandon a box that was connected to a stick that stopped people from registering that she shouldn't be going anywhere that she shouldn't be. Aunt Sharon hadn't even seemed to notice that the box was there even when she'd gone out to do the gardening; she'd just casually walked around it as though it had always been standing in her way and she'd grown too used to it to bother discussing it, even though it hadn't even been here last week.

But even if the box was proof that it was real- she might be the only one who could see it but it was too solid to be a hallucination-, she couldn't just put her life on hold as she waited for the Doctor-

"_Amelia Pond_!" a familiar voice suddenly called from the front of the thankfully-deserted house, accompanied by the honking of a car horn. "_Get your coat_!"

Amy didn't even stop to wonder at the timing of that call; taking only a brief detour to hurry into the house to pull on a dark blue coat, Amy hurried back out of the house and around to the front, coming to a halt as she took in the sight in front of her with a broad smile.

The Doctor, still dressed in that bizarre tweed jacket and bow tie, was standing casually outside her house, while behind him was an old-fashioned car- fold-up roof, wings over the wheels and lights on poles out at the front- in bright yellow, the Doctor leaning against it in a manner that made it clear he was at least able to drive it, if not its actual owner.

"Well, that's those few things picked up," the Doctor said, smiling casually at Amy as though he'd just popped out to get some food.

"You... you came back..." Amy said, staring bemusedly at him, momentarily unable to get past the fact that he was finally _here_.

"'Course I came back," the Doctor replied with a smile. "I always come back-"

The Doctor's further comments were cut off when Amy threw herself at him and wrapped her arms around his waist, burrowing her face in his shirt to try and conceal the worst of her tremors as she fought to stop herself from crying in relief.

_He'd come back_...

Not a few weeks, months, or even years later; he'd come back in just a couple of _days_...

"Th... thank you..." Amy said, her voice low as she stepped back to look at the Doctor with a broad, albeit trembling, smile.

"No problemo, Pond... and I am _not _saying that again; where did I get 'problemo'?" the Doctor asked, rolling his jaw as though he was trying to get a bad taste out of his mouth before he smiled at her. "Anyway, I assume the TARDIS is still fine?"

"Aunt Sharon's just been walking around it," Amy confirmed, smiling back at him. "It's like it was always there and she's been going it so long she's stopped complaining about it, really; it's... well, it's cool."

"'Cool'?" the Doctor repeated, smiling at her. "Of course it's cool, Amelia Pond; it's the TARDIS, it's always cool."

"By the way," Amy asked, looking at the car with an eager curiosity, trying to avoid further questions about her recent 'breakdown', "what's this?"

"Oh, this?" the Doctor said, smiling at her as he patted the yellow car affectionately. "This is Bessie."

"Bessie?" Amy repeated, staring at the car incredulously. "You named your car _Bessie_?"

"Nothing wrong with Bessie; it's a perfectly good name," the Doctor said, looking defensively back at Amy as he kept one hand on the car as though trying to stop it attacking Amy at the implied insult. "She's got _character_; you don't just find this sort of character in any old car on the street, you know."

"Hey, I love it; I was just... well, surprised that you had something so... _wow_," Amy said, smiling reassuringly at the Doctor before she turned her attention back to the car; it might be old-fashioned, but the Doctor's comment about the car having character certainly fit.

"Just remember that Bessie's a 'she', not an 'it', and your apology's accepted," the Doctor said, smiling warmly at her as he leapt over the driver's door and into the seat, before he reached over to open the passenger door. "Well, get on in, will you?"

Grinning broadly, Amy hurried around the car and leapt into the passenger seat, only to pause as she noticed a surprising lack of something important. "Uh... where are the... seatbelts?"

"Oh, don't worry about _seatbelts_; Bessie's equipped with a minimum inertia hyperdrive, absorbs all forward momentum and ensures that you'll never get thrown out of the old girl no matter how fast I go," the Doctor said, smiling nonchalantly at her. "Anyway, buckle up- I assume we've got some time before your aunt gets back?"

Amy's brief nod was all that the Doctor needed. "Right then; just to give you a quick demonstration..."

No sooner had the Doctor spoken than Bessie was suddenly in motion, leaving Amy feeling like she was pinned to her seat as the yellow car tore through the streets of Leadworth at an almost ridiculous speed, weaving neatly around other cars so quickly that it seemed like they barely had time to register that the Doctor was even there before he was gone again. Looking out of the window, Amy couldn't help but let out an enthusiastic whoop of joy at the sheer speed of their current transportation, the village that she'd lived in for so long whizzing past her eyes so quickly that she felt like she could see all of it in a matter of minutes-

"Test drive's over and here we are!" the Doctor said, the car coming to a halt so smoothly that Amy only realised they'd stopped because everything around her had stopped moving; the Doctor hadn't been exaggerating when he'd explained how the car could absorb momentum.

Glancing at the location where they'd stopped, Amy was slightly disappointed to see that they were just parked in front of a moderately-sized house that she recognised from a few of her walks around the village; it wasn't even that far from her own house, and she'd walked around this area in the past long enough to know that nobody lived here...

Then she noticed the 'Sold' sign standing in front of the house, and the implications of why the Doctor had come to a halt here became obvious.

"You... you're going to _live _here?" she said, looking at the Doctor with a broad grin.

"Well, I'll move in in a couple of hours- I've got a couple of friends bringing the furniture over for me-, but most of the paperwork's already sorted out," the Doctor said, smiling nonchalantly over at her. "As far as the rest of Leadworth's concerned, I'll just be somewhat-reclusive investment millionaire Doctor John Smith- I look just old enough to make the title convincing, after all-, who made some good money with the right investments in his youth but has decided to settle down for a quiet life for a few years before deciding what to _do_ with all that money."

"Investments?" Amy repeated, looking at him inquiringly.

"Well, most of it's just the compound interest I've collected from a bank account or two over the years, but it's not like I can say that I'm using money I left after winning a few good hands in a game with the Duke of Wellington-" the Doctor said, shrugging nonchalantly.

"_The Duke of Wellington_?" Amy interjected, staring at the Doctor with a broad grin. "You _met _him?"

"Oh yes; I actually helped win the Battle of Waterloo by convincing the leaders of both sides to take the right course of action- obviously I advised both sides at different points in my life, of course-, but that's a story for another time," the Doctor said, smiling warmly at Amy before he sat back in the car. "Now then, we've still got a few hours before anyone gets here, and I noticed a nice-looking roadside cafe a few minutes away; what would you say to a quick trip over there for a bite to eat before the house is ready?"

"Sounds good," Amy said, smiling back at the Doctor (She briefly wondered why he was going to some roadside cafe when Leadworth had a few promising cafes as well, but quickly answered her own question; it might attract too many questions if people saw her dining with the mysterious Doctor John Smith before he'd even officially moved in).

* * *

><p>"Now then," the Doctor said, sitting down opposite her at their table in the cafe after placing their order, looking at her with a casual smile, "if we're going to be preparing you for what's out there, best we get started; what's your first <em>big<em> question?"

"Well... if you're a time-traveller, can you... change things?" Amy asked, deciding to target the most obvious question; hopefully it would take her mind off that strange... _feeling_... she kept getting when the Doctor looked at her. "Like... you know-"

"Yes and no," the Doctor replied, looking firmly at her, his earlier relaxed manner vanishing as he stared intently at her.

"Uh... what do you mean?" Amy asked uncertainly.

"Yes, I _can _change things, but that doesn't mean that we _should _change things," the Doctor said, looking firmly at Amy, his previous smile replaced by a firm expression that made it clear that what he was about to say was something that it was vital for her to understand. "History is a very complicated sequence of events, Amelia Pond; helping to ensure that it maintains its proper course when others try to change it for their own ends is permissible, but attempting to change that sequence of events because you think it'll be better, or even altering a minor detail just because you want to, can be _very _dangerous."

"So... just to pick an example... what would happen if you... stopped Hitler coming to power?" Amy asked (She felt as though someone had once used that example for something, but she couldn't remember _who _or _what_...).

"I can't know," the Doctor said, shaking his head. "Maybe I'd stop the war and dismantle the Nazi party before it could start, or maybe I'd just remove the incompetent madman from power and have Hitler replaced by somebody who _knew _what they were doing and would be able to be a far more competent leader for Germany during the war than he was; there were so many people who only _followed _Hitler because they weren't sure who'd support them if they tried to stage a coup against him. Even if I tried to help the British on the other hand, who's to say I couldn't make things worse; I once had to undo an incident that changed history to create a timeline where Britain had conquered the world after fighting off an invasion in 1903..."

They paused for a moment as the cafe owner brought them their previously-ordered bacon sandwiches- Amy wondered about the slightly suspicious look she was giving the Doctor, but decided to ignore that-, but as she walked off, the Doctor resumed his explanation. "The point is, even if only a few moments are what we call fixed points in time- moments where what happened there and then are so important to the overall fabric of reality and the course of history that they _have _to remain intact-, the rest of history's moments are still so delicate that changing them is inadvisable in case they just make things worse in the long run, even if they only have limited effects immediately."

"I... see," Amy said, nodding slightly uncertainly at the Doctor; she didn't entirely understand that comment about 'fixed points', but she accepted the Doctor's explanation for their importance nevertheless, before she settled on her next question after taking a bite of her sandwich. "So... you _can _change history, but it's normally pretty dangerous?"

"Normally, yeah," the Doctor confirmed with a nod. "I mean, when I was younger I changed things when I accidentally caused an accident upon my original arrival somewhere, and another time I tried to save an expedition to a lost island that resulted in a movie actress in the 1930s nearly taking over the world in the seventies- although I was able to save the expedition in the end; I just had to ensure that she didn't survive the whole experience-, things like that..."

He shrugged dismissively before he focused his attention back on Amy. "I might have changed it by accident, but I've dealt with a variety of cases where someone has changed history on purpose and I've had to change it back; it's a difficult thing to balance, and the universe can sort itself out if the changes are small enough- someone meeting his wife ahead of schedule, things like that-, but you do _not _want to make a habit of doing that."

"Understood; changing history is a bad thing," Amy said, giving the Doctor a slightly jocular salute before she looked more curiously at him. "Uh... how do you... know when you're dealing with one of those... locked moment things?"

"How do I know when a point's fixed?" the Doctor finished for her, smiling in understanding. "It's something my people developed the ability to do over time; as Time Lords, it was our duty to ensure that history remained intact... before..."

"Before what?" Amy asked, looking at him as his smile faltered, the Doctor's head lowering as he suddenly appeared so much smaller and sadder than he had before, until he looked up at her with a more casual smile.

"Long story," he said, shrugging as though what had just happened was nothing important, even if the pain in his eyes made it clear that he didn't want to discuss it further. "It was a bad day- stuff happened-, and... well, let's leave it at that."

"Oh," Amy said, putting down her sandwich and reaching over to take the Doctor's hand in a comforting gesture that felt inadequate despite her lack of ideas about anything else that she could do.

"Was it... the Faction?" she asked, recalling the way he'd reacted when he'd first heard of even the possibility that they were still around.

"Among other things," the Doctor said, his expression a dark, grim one as he looked back at her, before he shook his head and grinned at her, his melancholy mood forgotten. "Anyway, enough of that; why don't you tell me a little about yourself?"

Amy knew that it was a poor ploy on the Doctor's part to draw attention away from his own past- even if he still wasn't giving her any details, he clearly had _some _kind of history with the Faction based on his conversation with Prisoner Zero-, but even with that knowledge she couldn't help but feel touched that he even bothered to ask that question; she was fairly sure that he would share what he knew with her when the time was right, but, after everything that he must have experienced in his life, the fact that he was still clearly interested in learning more about _her_...

A part of her reflected that she would have found this kind of attention disturbing if it had come from any other person of the Doctor's apparent age- she wasn't stupid, after all; she knew what kind of people you had to watch out for-, but when it came from her now-not-so-Raggedy Doctor, she...

Well, she didn't know _how _she felt about it, precisely, but she _did _know that she liked it; when the Doctor smiled at her or spoke to her, she felt... _strange_... but good strange... in a way that she'd never felt before with anyone...

* * *

><p>AN 2: OK, quick question; with the rest of this part of my series alternating between the Doctor and Amy's lives in Leadworth for the next few years and the occasional trip in the TARDIS, does anyone has anything they'd particularly like to see the Doctor and Amy encounter, do, or visit during this time frame?<p>

Just don't forget that 'Mels' has ceased to exist- for reasons that will be elaborated on later-, so anything involving her is out, but I will take other suggestions unless they drastically conflict with what I DO have planned for later.


	8. TARDIS Restored

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Another short time-jump, this one begins with the Doctor settling into his new house a couple of days after the last chapter

The History of Paradox

As he took in the house around him, the Doctor had to admit that he had chosen fairly well; it might not be as large as his old place on Allen Road, but it was comfortable enough for his current purposes, and Leadworth, while small, had enough to keep him comfortable for a while. After moving in, he'd made a few brief introductions to the locals who'd asked him about where he'd come from or what he was doing in Leadworth when he'd gone out to shop for supplies, but so long as he generally kept his head down and avoided attracting attention to himself as a person while he was out and about, people seemed content to dismiss Doctor John Smith as a harmless man with a unique taste in clothes and cars (A couple of children had seemed to be particularly appreciative of Bessie; he'd caught some comparisons between Bessie and 'Gumdrop', but once he'd recalled the car in question he'd appreciated the reference).

Right now, however, he wished that he had an explanation for the real problem facing him; the anomalies presented by the existence of Amelia Pond.

He doubted that even Amy herself was aware of the strange details surrounding her past; the way that she just said that her parents had died without providing any kind of information about _how _it had happened- not even making up elaborate stories about what had happened; she'd just said that they were gone and moved on so quickly that he hadn't felt right pressuring her- made it clear that there was far more to that situation than even she knew, and that house was far too large for just two people to go to the trouble of buying it, particularly given how little time Aunt Sharon seemed to spend in it...

The only problem was what he was going to actually do about that whole mess. While it seemed to be fairly obvious that the crack he'd closed upon their first meeting was the source of whatever had happened to her, that didn't explain what had caused the crack in the first place- the Faction wouldn't be that subtle; the presence of Prisoner Zero was apparently just an unhappy fluke, and if they'd wanted Amy for themselves they'd had seven years to take her due to the TARDIS's 'glitch'-, and it certainly didn't give him any clues about how to undo it, since the obvious possibility of just removing the source of the problem had clearly failed judging by their continued absence after the crack was lost.

Still... with no clues to go on, coupled with his refusal to leave Amy until she wanted him to go and his resolve to travel with her once she'd left school, there really wasn't much else that he could do to find the source of that crack, particularly when he now only had a basic scan of it that he'd taken with the screwdriver to go on.

This was definitely one of the many professional reasons that he missed the other Time Lords; without Temporal Observations back on Gallifrey keeping an eye on this kind of problem, he was limited in how he could track this kind of temporal distortion...

Trying to take his mind off things, the Doctor picked up a book and began to skim through it, but before he could get more than a few pages into the plot, he jumped out of the chair as he felt something burning in his pocket, reaching quickly in to pull out the TARDIS key, now glowing a brilliant yellow even as he looked at it.

"Oh, yes..." he said, grinning as he stood up and slipped the key into his pocket before he headed for the door, all thoughts of his earlier frustration forgotten in the face of this sudden good news. As soon as he was outside, he briefly contemplated taking Bessie, but the thought was discarded before it had even fully formed in his mind; leaving the old girl parked outside Amy's house wouldn't help their attempts to create the impression that they didn't know each other, and making two walking visits to that house on the same day could be noticed where one might be passed off as coincidence.

After a few moments of running, he found himself outside Amy's house once again, pausing only briefly to confirm that the car he'd earlier identified as her aunt's was once again absent before he walked around to the back of the house to knock on the back door, grinning as Amy opened the door to look at him.

"What?" she asked, smiling curiously at him; while the Doctor was settling in, they had decided to avoid contact with each other, although they were already making plans for Amy to take the occasional detour to visit the Doctor's house on days when she had no other plans (She'd mentioned a few friends she spent time with after school on some occasions, but she had also stressed that they didn't spend _every _day together, even if the Doctor had no problems with her doing other things with her life).

"Well," the Doctor said, holding up his key and pulling the TVG out of his pocket, where he'd been keeping it just in case of this situation, "I just got a little signal via _this _that my ship's finished rebuilding itself, so, if you've got some time to spare... care to see my time machine?"

The broad grin that she gave him in response was all that he needed to see to know that Amy had been eagerly waiting for this very chance.

He might not be able to figure out what had happened to her parents or work out the source of that crack, but he could _definitely _show Amelia Pond around the last TARDIS in the known universe...

As the two of them turned around and walked over to the TARDIS, the Doctor couldn't help but smile at the thought of what they were about to discover; he hadn't experienced the thrill of not knowing what the ship was going to look like _inside _for longer than he could remember (He'd witnessed it reconstructing from the inside after Compassion's last act had 'recharged it', and he'd seen it while it was recovering from containing Marnal's cold fusion generator, but on both those occasions it had been limiting the scale of the changes to cope with the fact that he was there, and every other time he'd changed the ship's interior he'd known what he was setting out to accomplish himself; he had literally _no _idea what to expect now).

"Just keep in mind that even I don't know _exactly _what we're going to find when I open this door- the old girl's been repairing herself since I last landed here and she's bound to take a few liberties, after all-, and all should be fine," he said, grinning over at Amy before he turned and opened the door, pointing the TVG at the darkened interior for a moment before it lit up, the small police box interior fading away to reveal a brand-new one.

"Oh," the Doctor said, grinning as he took in the sight in front of him, already appreciating the potential offered by the far larger console room before him. "Oh, you sexy thing..."

Grinning broadly as he hurried into the console room before him- the slightly orange lighting was a bit different, to say nothing of the multi-level structure, but he was sure he'd get used to it eventually, and he _definitely _appreciated the 'steampunk-esque' elements of the new console, given the unique contrast of a typewriter and gramophone alongside the more conventional controls-, the Doctor nonchalantly slid the TVG back into place before he turned to look at Amy as she stood at the door, staring incredulously at the TARDIS interior.

"Well," he said casually, "want to make any comments? Any passing remarks? I've heard them all."

"It's... it's _beautiful_..." Amy practically whispered, one hand reaching out to touch the wall as she walked forward for a few moments before she turned to hurry up the stairs, standing on the glass floor that the console was now positioned on. "But it's... how's it so...?"

"So big inside?" the Doctor finished with a shrug, grinning broadly at her. "Interior dimension is in a separate realm from the exterior; it's a whole branch of Time Lord science that your science doesn't even have the proper terms for right now, and we can cover that in a later lesson. Right now, we need to get on with moving the old girl somewhere more secure; feel free to keep talking while I get her moving."

"But..." Amy said, looking around the console as the Doctor quickly tapped a few controls to disable the temporal circuits- without a completely clear idea on how this new console worked, it was best that he take care to eliminate anything that might cause them to go too far afield on their first trip-, "but... why is it a phone box?"

"It's camouflaged," the Doctor replied with a shrug as he shut down the temporal circuits before moving on to shut down the galactic positioning system; anything that would help him focus the coordinates on Earth was a good thing right now, even if he'd have trouble turning them back on later. "And it's not a phone box, it's a Police Box, which was a special type of telephone box that policemen used to use before phones became more mobile than they are now; the old girl landed in 1963 a few centuries back, the circuit broke down- she still analyses surroundings in the first nanosecond to calculate a 12-dimensional data map of everything within a thousand-mile radius to determine which outer shell would blend in best with the environment; she just sticks with the police box-, and she's looked like that ever since."

"But... why does it look like it's made of wood?" Amy asked, still looking at him in confusion. "How do you change the bulb on the top? Do you _need _to change the bulb on the top? You've got a wooden time machine, don't you feel a bit... well, I don't know...?"

"Well, I did try fixing the chameleon circuit once or twice, but the first time the things it turned into still wouldn't completely blend into the environment and made it hard to work out how I was meant to enter it anyway- I mean, how do you _lock _an _organ_?-, and the second time someone hacked into the circuit and nearly gave me away by turning it into more conspicuous forms, so I decided to break it again," the Doctor said with a shrug. "Besides, I like the message it presents; just open the door and have assistance available on request, you know."

"Oh," Amy said, looking back at the doors behind her- still the same apparent doors on the inside as they were on the outside, the Doctor noted; he had to admit, that change was one part of these newer console rooms that he definitely preferred- before she looked back at him. "Why do you wear that?"

"Wear what?" the Doctor asked.

"The bow tie," Amy clarified.

"Ah," the Doctor said, reaching up to his neck with a smile. "Bow ties are cool."

"And... you're really an _alien_?" Amy asked, looking at him with a slightly tentative smile. "I mean, you're not from the future or something like that?"

"Well, by your perspective, I _suppose_ I'm from the future, but it's not the future of _this _planet, and our position in time in relation to the rest of the universe was always complicated to explain if you couldn't see things our way-" the Doctor began.

"Are you... a space squid or something?" Amy interrupted, suddenly looking more closely at him.

"What?" the Doctor asked, looking sharply back at her as Amy reached up to take his chin in her hands and tilt his face slightly so that he was looking more directly at her, allowing her to thoughtfully study his face.

"You know, a space squid," Amy said, looking at him with a slight grin. "Like in _Galaxy Quest_, with those disguise things, or... or are you like that little thing in the human suit from _Men in Black_? Is that why you walk like that?"

"Amy," the Doctor said, crouching down slightly and placing both her hands on either side of his face as he stared at her- he appreciated the raw imagination of humanity, but there were times when it inspired some truly bizarre questions-, "this is me; this is what I really look like, understood?"

"It is?" Amy asked, looking at him in surprise as she stepped back, tilting her head slightly as she looked curiously at him. "But... if you're an alien... I mean, you look human..."

"No, you look Time Lord; we came first," the Doctor said, standing up with a nonchalant shrug.

"And that means that you get to go first?" Amy asked, rolling her eyes slightly as she stared at him, even if the slight smile on her face showed that she didn't mind the slight dig.

"Well, actually, it's more like our evolution created a morphic field that made it more likely that the next races to evolve would follow the pattern of our physical make-up- why fix what isn't broken, after all?-, even if there's still some debate about whether that was totally natural..." the Doctor said, his voice trailing off before he shook his head and looked back at her with a broader grin. "Anyway, that's for another lesson; right now, I just need to perfect a _short _hop..."

For the next couple of moments, his concentration was completely focused on piloting the ship as he ran from one panel on the new console to another, his focus exclusively on the controls in front of him, taking care not to overshoot his destination or spend too long in the vortex; given his current rule about ensuring that Amelia was fully-trained before they started travelling together, the last thing he wanted was to overshoot...

"Done," he said, grinning as the central time rotor came to a halt, leaving him to nonchalantly walk over to the door and open it to reveal his new house's sitting room, grinning back at Amy as she looked at the new location waiting outside their doors

"_Wow_..." she said, grinning as she walked out of the ship, the Doctor emerging from the TARDIS as she walked around the exterior with a broad grin before she looked at him. "It really _is _bigger on the inside..."

"'Course it is," the Doctor said, affectionately patting the TARDIS's form as he did so (He'd probably need to remove the TVG later to limit the possibility of the old girl being tracked, but until then he'd focus on the good news of having her back rather than worry about the finer details like that). "The old girl's been my home for centuries; be a bit stupid if she _wasn't _bigger on the inside, really."

"I can guess," Amy said, grinning at the TARDIS once again before she turned back to the Doctor. "So, since Aunt Sharon's away for the next day or two, and school's starting soon... any chance today's lesson could involve a tour of this thing?"

"Amelia Pond," the Doctor said, grinning back at her as he walked around to open the door once more, "it would be my pleasure."

So long as he kept an eye on the time- and the old girl wasn't _too _annoyed about being cut off from her interior dimensions; she might understand why he'd had to do it but that didn't mean she'd like getting cut off after everything he'd put her through during his last regeneration-, there should be enough time to show Amy some of the more interesting parts of the TARDIS before she had to get home; if he was quick enough, maybe he could even try and whip her up something to make up for the food he'd eaten during their first meeting...

* * *

><p>AN 2: Hope you enjoyed that; next chapter, we'll look at Amy's thoughts on the TARDIS interior as she goes back to school, as well as our first look at Rory in this new timeline<p> 


	9. The Mysterious Mr Smith

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: I'm taking a few guesses about where Amy and Rory went to secondary school, but given that they were still living in Leadworth in their early twenties I'm assuming that there was a bus service or something that they used to get to a school in a larger city nearby (It's not without precedent, either; I had a friend in senior school who lived in a small town about an hour's bus-ride outside the city, and he still managed to get into school in time for morning classes)

AN 2: Hope you like this chapter; I had a few problems with some of the fine details, but I think the final result worked out well, and hopefully things should be more straightforward in the next chapter

AN 3: Once again, if anyone has anything that they'd like the Doctor to encounter in this time period, let me know and I'll include it if I can

The History of Paradox

Even as she sat at her desk taking notes, Amy couldn't really bring herself to focus on what she was doing; after what she'd done in the last week of the holidays, geography wasn't exactly at the top of her priorities list right now.

She'd been inside a _time machine_...

She was trying to concentrate on her work, of course- the Doctor had promised to help her with her homework if she needed it, but it wasn't like she wanted to completely depend on him for everything-, but it was so hard to think about the fine details of geography when she was so busy thinking about the incredible interior of the Doctor's TARDIS.

How could she be expected to focus on glacial or volcanic formations when she'd spent time in a machine that defied virtually everything almost everyone else on Earth knew about the laws of physics? The ship had not only been bigger on the inside than it was on the outside, but there'd been so many incredible rooms within it; an art gallery featuring art that the Doctor had apparently recovered from the disasters that history stated had destroyed them, a library filled with virtually any kind of book that Amy could imagine, a vast wardrobe with clothes ranging from what looked like ancient Rome to what Amy presumed was the far future, a kitchen that resembled an Italian restaurant...

The room that had most immediately struck her in the machine, however, was what the Doctor had called the 'Room of Remembrance'; even if he hadn't intended to show it to her, once she'd opened the door, it wasn't something that he could pass off.

Thinking about the implication that there had been other people in the TARDIS apart from her and the Doctor was slightly disappointing, of course- it made her feel slightly less special; she was just the latest person in the TARDIS rather than the first one-, but, in the end, the fact that she was there in the first place was more than enough to make up for that; who cared who'd been there before? She was here now, and that was what mattered; everyone else who'd travelled in the TARDIS before her had played their part, and that was the main thing.

That secondary 'memorial table' was something that had really struck her, however; a shattered star badge, a dark toga, a badge with 'SSS' on it, what looked like an out-of-date history textbook on the French Revolution, a guitar, an orange cardigan, a suit of what looked like blue armour, a leather jacket, what looked like an earpiece...

It might have been significantly smaller than the other table, but that didn't mean that Amy hadn't been able to work out what was the difference between the two tables; one was just to help the Doctor remember those who'd moved on to make lives after him, and the other...

Well, the other was for those who hadn't had the chance to make lives after him.

It hadn't changed how Amy felt about her desire to travel with the Doctor- if nothing else, that table was a lot smaller than the other one, so when you got down to it the odds were still in her favour that things would go well-, but she did appreciate why he was giving her these lessons more than she had previously; if she was going to travel with him, he wanted to make sure that she knew everything that she might need to survive anything that they might encounter in their travels.

It might be tedious to continue going to school, but if it meant ensuring that the Doctor felt comfortable taking her along, she'd put up with anything; even after he'd shown her the TARDIS interior as an example of what he was capable of, Amy was certain that his ship still had a lot more to share with her...

Right now, however, she wished that she could skip through this whole tedious lesson; after spending time looking around an actual time machine, learning about the geography of Earth seemed almost boring by comparison. She knew that she couldn't share what she'd seen recently with anyone else, but she had to get through school if she was going to travel with the Doctor like she wanted.

Of course, getting to school was still difficult given the time it took to travel in the bus, but it was still a tedious bit of work. A part of her wished that she could just use Bessie to get a lift in each day- not only was the Doctor's car far more interesting to travel in than the bus, but it was also a lot faster-, but she knew why they couldn't do that; Amy Pond getting a lift into school from Doctor John Smith in that distinctive car of his would raise far too many questions...

_God_, it was hard to keep track of everything that they had to take care of sometimes; if she needed any more reason to enjoy weekends, it was the fact that she wouldn't have to lie about what she was doing to anyone.

"Amy?" a voice said from off to the side, drawing Amy's thoughts back to the present as she looked around and noticed that the rest of the class were walking out. "Are you OK?"

"Mmm?" Amy said, turning to look at the source of the voice with a smile. "Oh, Rory... yeah, I'm fine; just... thinking, you know?"

"About what?" Rory Williams asked, looking down at her workbook with a slight smile. "No offence, but you don't seem to be doing much work."

"What?" Amy asked, glancing down at her jotter and biting back a curse when she realised that Rory was right; she'd made a few notes on the essentials of what they'd covered in class today, but she'd been so caught up in thinking about the TARDIS that she'd not been paying complete attention to what was in front of her.

"Oh, this?" she said, laughing it off with a smile. "Just... making sure I got it all straight up here before I write it all down; making notes during class isn't always easy, you know?"

It wasn't much of an excuse, but as she took a few quick glances at the board to get down what she could as Rory headed for the door, it was the best that she could come up with; if she was quick, she could probably get down a _couple _of things before she had to leave, and then the Doctor could help her work on the rest of it...

Maybe it was slightly cheating to ask an ancient time-travelling alien to help you with your homework, but as far as Amy was concerned, she was just picking a friend's brains for a few extra pointers; if the Doctor's ability to make anything fun when he was talking about it wasn't a good excuse to ask for his help, Amy didn't know what was.

* * *

><p>As he watched Amy get off the bus that had taken them back to Leadworth, Rory couldn't help but wonder what had happened to his best friend (Even if a part of him would always want more, he'd learned to suppress that over the years; mentioning it would just make things awkward and it wasn't like she saw him that way anyway). Ever since that thing with the sun going weird a couple of weeks ago, Amy had seemed to have... changed somehow, was the best way that he could describe it.<p>

While she had always smiled and tried to appear happy in the past, he'd always felt as though something had been missing; even now, a part of him had always suspected that he knew what it was that she didn't have, but the rest of him...

Well, the rest of him had just wanted to be part of her life.

He wasn't sure how it had started, really; whenever he tried to look back at how their friendship had started, it felt like a blur, as though the moment when they'd started to be friends had been so simple he hadn't thought it worth remembering at the time...

Ever since that strange day when the sun had changed for a few minutes, Amy had been acting... different. She'd never exactly lost her old confidence- all those stories she'd told as a kid when only he and... when he was the only one who ever listened to her were proof enough of that-, but she seemed to be far more assertive now than she had been before, as though she'd suddenly discovered that she was right about something.

However, the puzzle that really occupied Rory's mind, as he started to walk home after getting off the bus himself, was what could have happened that Amy wouldn't tell him about... and why was she walking in completely the wrong direction to get to her house?

Glancing at his watch, Rory noted that he still had time to get home- his parents were never exactly that concerned if he was a few minutes late given how erratic the bus could be getting them back; it was only if he was more than an hour behind schedule that they started getting worried-, and promptly began to walk after Amy, keeping enough distance between her and him to prevent her immediately noticing him if she happened to turn around while still allowing him to keep an eye on her.

After a few moments of walking down a street Rory vaguely recognised- Leadworth might be a small place where it was easy to see most of it in a short amount of time, but that didn't mean you took everything in-, Amy turned and walked into a house that Rory vaguely recognised as one that had been sold recently; he'd noticed the sign while he was out walking once or twice, but since he'd never had a reason to pay attention to it before he couldn't be certain...

After a few moments of quick contemplation, Rory hurried over to the house, and- after taking a quick look to confirm that nobody seemed to be at the windows or in the street nearby- crouched down and hurried towards the nearest window, taking up a position that would allow him to peer inside while hopefully not attracting attention to himself.

Whatever he'd been expecting to see, it hadn't been the sight that greeted him; Amy, sitting casually at a desk, writing away in her jotter while occasionally looking up at an older man sitting opposite her, the stranger looking up from the book that he was reading to smile casually at her and answer whatever question she'd posed. The man seemed to be about a decade older than Amy, and was dressed in a tweed jacket, dark trousers, and a light blue shirt, along with a dark blue bow tie.

Now that Rory thought about it, the man he was looking at _did _match the description he'd heard of that new 'Doctor John Smith' who'd started living in the village recently; apparently he'd made some good investments and decided to settle down in Leadworth for a while until he decided what to do with himself...

But what was _he _doing spending time with Amy?

For a moment, Rory's mind flashed to the horror stories he'd glimpsed in the news before he was even old enough to know what the stories were talking about- Amy was beautiful, even if he'd always stopped himself thinking about it; he knew that she didn't see him that way, after all-, but he stopped that thought before it could really start; Amy was too stubborn to accept anyone trying to do... _that_... with her...

Besides... as strange as it seemed for him to make this kind of snap judgement about someone... Doctor Smith didn't _look _like the kind of guy who'd do something like that.

He was wearing strange clothes for someone his age, of course- he looked like he was about go off to a fancy-dress party as some Victorian-era professor, or one of those stuffy old teachers who sometimes saw who should have retired long ago and didn't realise that fashion had moved on since their days as students-, but that wasn't exactly an automatic red flag; he could just have strange taste in clothes without actually being... anything like that.

Besides, Doctor Smith seemed to be doing nothing more than occasionally answering Amy's questions about what Rory assumed was her homework- he couldn't exactly see what she was writing in from his current position and didn't want to try and find a better one in case he attracted attention to himself-, and even then he didn't spend that much time looking at Amy.

Rory knew that he wasn't exactly an expert, but nothing he saw here suggested that Doctor Smith was... trying to get Amy to do... something... _wrong_...

He didn't even know what he was really worried about, but something about what he was looking at, even if it didn't seem that Amy was in any actual danger, still made him feel strangely depressed, as though he was witnessing the end of something even if Amy seemed happy to talk with Doctor Smith about whatever they were talking about...

Still, when he looked at everything, Doctor Smith didn't give the impression that he was doing anything other than helping Amy with her homework, and Amy gave no impression that she was worried or forced to be here; actually, judging by the way she'd been walking after leaving the bus, she was probably happy to be here.

In the end, there wasn't anything else for Rory to do but accept the situation presented to him and walk away; he didn't know enough about the situation he was looking at to feel comfortable telling Amy that he'd followed her, and nothing that he'd seen suggested that Amy was in any actual _trouble_. He'd keep an eye on her, and let someone know if it looked like anything had happened, but...

So long as Amy seemed happy, that was the important thing.

So why did he feel so depressed about that decision...?

Shaking his head after taking a last look at his friend, Rory sneaked back to the garden gate and then walked off back towards his house, forcing his mind back onto his homework rather than the sudden mystery of Amy's friendship with Doctor Smith.

If Amy wanted to tell him about it, he'd let her tell him in her own time; right now, he just wanted to focus on something less depressing than the idea that Amy suddenly had secrets from him.

* * *

><p>AN 4: To anyone who thinks that Rory should recognise the Doctor from Amy's stories, keep in mind that he's spent years picturing the Doctor as the 'Raggedy Doctor' without ever meeting him in person; without the ripped clothes of his previous self, the Doctor wouldn't exactly be that visually distinctive<p>

AN 5: Next chapter, we jump forward a few months, as the Doctor takes Amy on her first trip in the TARDIS...


	10. How to Coach Fish via Time Travel

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: A jump forward of a few months, including an overview of the intervening time before the Doctor and Amy travel to a very particular planet for an adventure that will be _very _different from canon, to the point where the Doctor won't even meet the same people he met originally...

AN 2: Points to anyone who can recognise the show that Amy quotes here

The History of Paradox

"_Yes_!" Amy said, smiling as she walked through the door of the Doctor's house, grinning as she tossed her schoolbag into the corner and casually tossed her blazer onto the nearby coatstand.

"Good news, I take it, Amelia Pond?" the Doctor asked, leaning out of the living room of his house to smile at her.

"Passed everything!" Amy said, grinning broadly at him. "They might not count towards the final marks, but I passed!"

"Good for you, Pond," the Doctor said, grinning at her as he walked out of the living room to talk to her more directly, his braces hanging by his side and his jacket on the hatstand in the hall.

As the school term progressed, they'd fallen into a routine of Amy coming over to the Doctor's house at least once a week whenever Aunt Sharon was in Leadworth and her visiting the house on a more regular basis when her aunt was absent, although she occasionally visited a few acquaintances from school when circumstances allowed (She sometimes had a nagging feeling that she would have liked some friends among the girls of the group, but Amy had always pushed that thought aside as irrelevant; she'd been fine with Rory as her friend when she was younger, and she was even better now that the Doctor had come back into her life).

"Most of the time people only really care that you passed, anyway, but it's good to apply yourself to what you like," the Doctor said, shrugging slightly. "I only just passed my exams to become a Time Lord when I was at the Academy and I turned out fine- not that I'm suggesting you be satisfied with a narrow pass, of course; when it came to my doctorate I took my studies _very _seriously-"

"_You_ only _just _passed your courses?" Amy said, staring incredulously at the Doctor; the idea that he could ever only 'just' pass something seemed almost impossible to her.

"Keep in mind that most Time Lords just stuck to what they needed to know and left it at that; can I help it if my studies suffered because I felt like looking up information that wasn't automatically relevant to a life where I would be expected to just hang around on Gallifrey and do a few specific jobs?" the Doctor said, smiling at the memory in a wistful manner before he looked more seriously at her. "Now then, since I'm pretty sure you don't have any actual work for the holidays- or at least nothing that can't wait-, what would you say to a quick Christmas trip?"

"A trip?" Amy repeated, looking at him in confusion before inspiration struck her. "What do you- _you mean_-?"

"The TARDIS?" the Doctor finished for Amy, grinning at the smile on the young girl's face. "Of course; I've worked out a few locations that should be perfectly safe for a brief visit while being interesting at the same time, so all we have to do is go in there, take a quick poke around, and then we're back here before anyone knows we're gone. Are you interested?"

"Do lemmings like cliffs?" Amy replied with an enthusiastic grin as she grabbed her coat and ran through the Doctor's house towards the door leading to the garden, glancing back to see the Doctor hurrying after her with a broad smile on his face as he shrugged on his tweed jacket.

"Not one of that show's better phrases, but the point is valid," her mysterious friend said, grinning as he walked out of the house and headed for the ship, opening the door to reveal the massive interior that made Amy feel like she was walking into a technological Narnia, the Doctor walking over to the central control console to indicate a small box on one panel. "No need to worry about us getting lost; so long as only make one trip at a time, I can easily get us back with this."

"What is it?" Amy asked.

"The Fast Return Switch," the Doctor clarified with a smile. "Press it once, and the TARDIS automatically returns to the location that it was at prior to its current location; so long as we don't keep the switch pressed down or go to too many locations before we want to come back here- the thing has a habit of getting stuck if it's pressed too often too quickly-, it's perfectly safe."

"Don't press the switch too much; check," Amy said, nodding at him with a smile as the Doctor turned his attention back to the console as a whole and started to flip the relevant switches, moving rapidly around the console as Amy watched him. "So... where are we going?"

"Oh, a very interesting-sounding planet; the planet Ember, around Christmas time in the forty-fourth century," the Doctor said, grinning over at Amy as he flicked the last switch and looked back at her. "Human colony, but it's got a rather unique ecosystem; they've got actual flying fish, can you believe that?"

"Flying fish?" Amy repeated, looking at her friend in surprise.

"Oh yes; the planet's uniquely-electrified atmosphere allows these fish to essentially swim in the air like it was water," the Doctor explained, still smiling at Amy before he shrugged. "No idea how they do that, of course- main reason I'd like to visit; maybe we'll have a chance to take a look and find out-, but it should be interesting to see even if we can't find the answers, don't you think?"

"_Brilliant_," Amy said, grinning enthusiastically at him.

"My thoughts exactly," the Doctor said, nodding in agreement at her. "Well then, let's be off; new discoveries await, after all."

Amy was so excited about the thought of her first trip that she almost didn't notice when the central column had stopped moving; it took the Doctor actually going over to open the door to help her realise that he was no longer piloting the ship, and then he opened the door onto a new and different world.

Not only was snow covering the streets in a manner that Amy hadn't even seen on the best Christmas she could remember- the roads were always cleaned too quickly for her to enjoy the picture of a completely white world, even if she recognised the need to keep the roads clear for drivers-, but the buildings were an intriguing combination of Victorian-like size and modern conveniences, elaborate stonework with all kinds of other technological additions on top of it, the sound of carols in the distance...

"_Wow_!" Amy said, grinning with joy as she looked over at the Doctor. "This is... _brilliant_!"

"Glad you like it," the Doctor said, smiling at her as he looked at the street around them, filled with people in clothes that reminded Amy of Victorian-era films with a slightly modern 'edge' to them that she couldn't quite identify, carrying bags and boxes with hints of wrapping paper in such numerous quantities that it was clear that they could only be preparing for Christmas...

Then a strange sound came from the TARDIS's still-open doors right behind them, prompting the Doctor to hurry back into the ship and head for the console, quickly bringing up the console screen and analysing the results.

"What is it?" Amy asked, looking anxiously at the Time Lord.

"There's a ship in distress above us," the Doctor said, turning away from the console to look at her. "When it passed too close to the planet's atmosphere, the electro-magnetic energy triggered a malfunction in the ship's engine's energy matrix; the ship's coming apart."

"So... that ship's going to crash?" Amy asked, looking at the Doctor in shock.

"Basically, yes," the Doctor confirmed, as he looked grimly at her. "The ship's too unstable for us to land there and reprogram the engines directly- those ships can be reconfigured based on the preference of the owners, so there's no way to determine where a clear area to materialise would be even if I could be sure of finding the right coordinates-, so we need a way to stabilise the atmosphere and bring the disturbances back to a manageable level that the ship can navigate; if we just had a way of transmitting the appropriate signal, we might be able to use the fish to generate a new wave-form that would cancel out the disruption caused by the atmosphere..."

"Uh... you mean, we use the fish to get the ship back into place?" Amy asked, looking uncertainly at him. "Like... like dolphins carrying shipwreck survivors to safety?"

"That's a good analogy, actually; let's go with that," the Doctor said, nodding in approval at Amy before he turned back to study the screen. "Well, according to this, we're in Sardicktown, one of the major population centres on the planet, so that should increase our chances of being able to find something useful to sort this situation-"

"What makes you think there _is _a way?" Amy interjected, only to realise what she'd said. "I mean, I'm not saying I don't _want _to stop it, but-"

"Always good to know what we've got to work with rather than making assumptions, Pond; good question, to which I have just as good an answer," the Doctor replied.

"Which is?" Amy asked, secretly delighted to see the Doctor so animated; it was as though she was seeing what he should be like, rather than the occasional moments of melancholy he seemed to slip into when he thought he was on his own...

"With those fish flying around up there, there has to be some way for someone to control the atmosphere's electrical field down here or we'd have fish flying into people's faces, and that's without taking the more potentially dangerous creatures up there into account, to say nothing of the storm itself; they probably use the Victorian design to limit the possibility of the storm interfering with anything," the Doctor explained, as he indicated the sky up ahead; looking up, Amy could just about see small specks 'swimming' through a surprisingly blue night sky if she stared hard enough. "If there _is _a way to keep the fish contained up there and limit the electrical interference down here, there should be a way to keep the ship up in the air..."

Hurrying back into the TARDIS, the Doctor activated a screen above the console and began to rapidly hit control switches on the panel before him, thoughtfully studying the information displayed on the screen for a few moments before he looked back at Amy. "There's definitely something in this town generating the wave necessary to stabilise the atmosphere up there, but it's not showing any signs that it's been used for anything other than maintaining this status quo for years, and this incident we're facing right now isn't the kind of thing that could just happen occasionally; given the time frame we've got available to us to sort this mess before that ship reaches the ground, I don't think we've got time to convince the person who's never used the equipment to start using it now, so that means we're going to need to make our own way of doing this."

"How?" Amy asked, looking at her friend in confusion. "Make our own?"

"Maybe..." the Doctor said, smiling thoughtfully as he studied the screen before him, tapping the sonic screwdriver against his chin in a contemplative manner for a few moments before he snapped his fingers in inspiration. "_Got it_!"

"Got what?" Amy asked, as the Doctor reached into a compartment inside the console and pulled out a small round object with a yellow light on the top that he quickly passed to Amy, along with something else underneath the object in question that she couldn't immediately see.

"Just step outside the TARDIS and hold this, will you, Pond?" he asked, looking at her with a reassuring smile that even the firm stare on his face couldn't detract from. Stuck for anything else to say in the face of the Doctor's straightforward request- if it had come from anyone else, Amy would have considered it a demand, but coming from the Doctor made it seem less insistent while still making it clear that this was something she should go along with.

"Uh... what are you doing?" she asked, looking uncertainly at him as she walked out of the ship, looking back at her friend through the still-open door as she stopped outside.

"Just got to make a quick hop back, but I assure you that it's all under control," the Doctor said, grinning reassuringly at her. "The Fast Return Switch is active, the TARDIS has stabilised, and you'll have this little homing circuit for me to focus on if either of those go wrong; just give me a moment, and I'll be _right _back!"

Amy just had time to grab the object that the Doctor had thrown at her and register that it was his TARDIS key before the ship's doors had closed in front of her and the police box began the wheezing, groaning sound that she had remembered and waited for over so many years...

Amy barely had time to start worrying that the Doctor was going to leave her behind before the TARDIS suddenly seemed to start becoming solid once again, the fade into nothing that she had first seen so many years ago never completing its transition as it returned to full corporeal form, prompting the Doctor to walk out with a casual smile as he brandished what seemed to be the lower half of the sonic screwdriver in his other hand.

"_Perfect_!" he said, grinning at her before his expression faltered slightly at the sight of the object in his hand. "I mean, I would have preferred not to lose the sonic, of course, but that's the way of things-"

"You lost the sonic?" Amy repeated, looking at the Doctor in confusion. "What did you do?"

"Oh, nipped back in time a good few decades, checked up on the machinery that we need while it was being built, and then hopped forward a decade or so from then to draw one of those floating sharks down so that I could slip one half of the sonic into it," the Doctor explained, wincing slightly as he studied the damaged screwdriver in his hand. "It's a roundabout way to do it, but it's all under control; now that I know what signals are being sent from that machine, we can use this part of the sonic and the TARDIS to transmit the necessary signal to get the ship back into position.

"Oh..." Amy said, smiling slightly as she took in what the Doctor had just told her. "So... the part you've got is still connected to the part in the... shark... that swallowed it?"

"No need to worry about it being digested, Amy; the sonic's built to cope with tougher conditions than a shark's digestive tract," the Doctor explained, smiling slightly as he looked up at the sky. "And the _best _part is that it's not even changing history; I never looked to see if I could or couldn't do this before I went back in time to set up the events that would allow me to do this now, so for all I know I was always able to do this and I just had to find out about it by setting it up."

"Oh," Amy said, looking thoughtfully up at the sky even as the Doctor ran into the TARDIS, leaving her to hurry in after him as he placed the screwdriver in a small hole in the console. As Amy watched, the Doctor pulled up the TARDIS monitor and began to study the readouts, turning a few dials as the screwdriver glowed a brilliant yet reassuring green; Amy thought that she could actually _hear _the electrical storm outside the ship's doors beginning to change as the Doctor channelled the necessary signals through the screwdriver.

"Is it working?" she asked after a few minutes had passed, the Doctor still occasionally flicking switches even as the image on the screen in front of him adjusted to respond to his commands.

"Just about..." the Doctor said, his eyes narrowing as he stared contemplatively at the information before him. "Just give me a few moments; we've got to get these readings _exactly _right, or the fish won't be present in sufficient quantities..."

Finally, after a few more moments of waiting, the Doctor smiled and stepped back, grinning over at Amy as he pulled the screwdriver out of the console.

"There," he said, tossing the half-screwdriver into the air and catching it. "Done and sorted; the ship's on its way back into space, in a fully stabilised orbit, and all we need to do now is find someone to give this to in the event something like that happens again."

"You think it will?" Amy asked.

"No harm in making sure, anyway," the Doctor said, smiling at her in that way that always made Amy feel strange inside before he headed for the door, Amy hurrying after him. "Besides, we've still got to see if we can get a chance to take a look at those fish; might as well spend time meeting a few new people while we're at it."

Amy didn't even bother to hide her enthusiasm for that idea as they began to walk down the street, introducing themselves to everyone they met who seemed interesting to talk to; after so long being regarded as the strange Pond girl, Amy couldn't even _begin _to describe how much she enjoyed this chance to get away from the same dull routine and witness this new world around them.

Everyone else just got to enjoy trips to other countries at best during the holidays; when she was with the Doctor, Amelia Pond got to go to different _planets_...

So why did she still feel that there was something else the Doctor could do for her?

* * *

><p>AN 3: Hope you liked that; the time-travel elements of the original 'Christmas Carol' might have been more interesting, but with the Faction to take into account, the Doctor is significantly less comfortable about changing history than he was in the original story...<p>

Next up, a quick encounter between the Doctor and Aunt Sharon...


	11. Another Distant Guardian

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Another jump forward of a couple of months, this time focusing on the Doctor as he finds himself dealing with some of the more tedious parts of modern life, as well as running into a _very _particular person (A bit uncertain abot the result, but I think what I came up with worked...

AN 2: On a minor note, the Doctor's reference to him opening a restaurant occurred in the Fifth Doctor novel 'The Crystal Bucephalus'

The History of Paradox

As he walked through the local Leadworth shopping centre- they'd basically stuck the supermarket equivalent in with a bunch of other ships, but it wasn't quite large enough to qualify as a 'market' on its own-, the Doctor almost couldn't believe the sheer normality of what he was doing right now; after centuries of generally picking up food from the TARDIS kitchens- starting with food from the food machines and developing from there to incorporate a more elaborate kitchen-, the idea of actually _cooking _for himself was almost as alien to him as the TARDIS would have been to anyone else.

Admittedly, it wasn't like he couldn't still use the TARDIS to provide his meals, but he didn't want to grow too dependent on that function of the ship; if he was going to live in Leadworth for the next few years, he needed to at least occasionally visit the local shops or people might start to ask awkward questions.

Besides... when the ship tended to produce the same meals most of the time- the kitchens could adapt to new companions' personal tastes, but there was only so many 'recipes' that the TARDIS could store in its databanks, particularly after so much non-essential data had been sacrificed when Compassion had helped to restore it to normal after the mess in Avalon-, it couldn't hurt to try and acquire the opportunity to experiment; he'd done it all the time when he'd first opened the Tempus Fugit six bodies ago, before it had acquired enough of a reputation to merit him hiring additional chefs, so why couldn't he get back into the swing of things now?

In some ways, it was nice to get back into a more peaceful, less high-stakes-demanding situation after the mess with that spaceship on Ember; the aftermath had been enjoyable enough, and he and Amy had enjoyed the chance to mingle with the general population- Kazran Sardick, the head of the local community, might sound like a fundamentally selfish person, but it seemed like he was generally willing to leave people alone to get on with their own lives unless they owed him something-, to say nothing of Amy enjoying his attempts to lure a few fish into the TARDIS for closer analysis (Their research had been limited as neither of them wanted to actually _dissect _the animals, but it was still fascinating to take a few readings of how the fishes' gills took in certain elements of the electrified atmosphere, or how their tails had been designed to move against the electrical currents in the atmosphere rather than water)-, but working out how to stop that ship hadn't been easy.

It wouldn't have been _that _hard to change history to sort the problem, of course; an additional unique side-effect of Ember's electrified atmosphere was that it caused a slight disruption in the time vortex where Ember was located, which meant that the web of time was slightly more malleable there than it would be in other parts of the universe, and theoretically he could have at least tried talking to the person in control of the equipment to work out what argument would have the most chance of convincing him to save the ship...

But he couldn't do it.

It might have been possible to find the man who owned the equipment and either convince him to operate it or go back in time and encourage him to become someone who would operate it, but those were the Grandfather's tactics; even if he could be sure that it wouldn't damage the Web of Time, he would _never _allow himself to try and change history because he thought things might be better afterwards.

He was the Doctor, the man who helped others when he could, but if he kept on going back and rewriting what he didn't like, he was no better than the Daleks or the Master, rewriting the book when the world didn't show him what he wanted to see.

He might have regenerated three times since the him that would have become the Grandfather, but there was always the potential for the transformation to take place, locked away in that dark part of his mind...

Still, right now he wasn't concerned about that; what mattered was that he was working on making a kind of normal life for himself for the next couple of years until Amy was ready to travel with him full-time. Money wasn't an obvious problem right now, anyway- with Anji's help he'd set up enough investments to keep him well-funded if anything serious came up, and the Brigadier had subtly contacted some of his remaining sources in UNIT to provide the Doctor with a retaining account to provide him with some money for immediate spending-, and he'd picked up various books from the TARDIS library and stacked them on the shelves to give casual visitors the impression that he was researching something, but working out some of the finer details of this whole arrangement was surprisingly difficult.

Making sure that he stayed in one place in the house long enough to give the impression that he was sleeping regularly in case any late-night walkers consistently saw his light on wasn't too difficult- he sometimes took advantage of the opportunity to fix a few parts of the TARDIS, although he continued to avoid the chameleon circuit-, but working out whether he wanted fresh or dried pasta when shopping for food was one of those minor details that the Doctor was surprised to find was trickier than expected; fresh took less time to cook, but he found himself preferring the taste of the dried pasta once it was completed, even if it took a bit more time...

He might have opened up a restaurant in a past life, but it was somehow trickier working out what was an acceptable range of dishes to acquire for a single person without any special occasions to celebrate; picking out something appealing to his tastebuds that could be thrown together in around a quarter of an hour or less was surprisingly tricky...

The thing that sometimes puzzled the Doctor the most about his current situation, however, was how little he really minded it.

He'd become frustrated with being stuck on Earth during the first few hours of his exile in his third incarnation, and now here he was, with the _ability _to leave Earth whenever he wanted and no regular threats to keep himself distracted, and yet he was perfectly fine setting up a house in this small village just to wait for a young girl to be old enough and trained enough to travel with him?

All right, so he could tell himself that he was doing it because he was lonely after so long travelling by himself and he wanted to make sure that his next companion would be better able to look after herself than the previous ones had, but that didn't mean that he was obliged to wait for Amy Pond to be that specific companion; the mystery surrounding that crack was only part of the reason he was staying here...

Lost in thought as he turned a corner, the Doctor almost walked into a woman coming from the other direction, nearly dropping his basket- he didn't buy enough things each time to make it worthwhile to get a trolley-, stepping backwards and pausing as he quickly checked his basket to make sure he hadn't dropped anything. Looking up at the person he'd almost run into, the Doctor found himself facing a dark-haired woman with broad shoulders and a stern yet smooth face, although her blue eyes were looking at him politely enough (Fortunately only looking at him with idle curiosity; he'd attracted so much of _that _kind of attention in his last body it was nice that this one seemed to attract relatively less of it so far...).

"Sorry about that; all my fault, wasn't looking where I was going," he said, slinging the basket under one arm and shaking her hand politely with the other one as he smiled awkwardly at her. "Doctor John Smith."

"Sharon," the woman replied with a slight smile as she shook the Doctor's hand in return. "Sharon Westwood."

The Doctor's smile faltered as he took in the name she'd just given him.

He was talking to Amy Pond's aunt... and it was one of those rare occasions where he had no idea what he was going to do now.

On the one hand, Sharon didn't know who he was beyond his official role in Leadworth of that reclusive young rich investor who'd brought a house to settle down for a few years while thinking about what he'd do with himself, but on the other hand, this was the woman who'd virtually neglected Amy while she was growing up, even after taking her in.

Even if Time Lord families and houses didn't operate under the same 'rules' as human ones, that didn't mean that he couldn't sympathise with Amy's plight; to be so neglected and ignored by their own relatives...

He wasn't entirely sure if he or Amy would have had it worse growing up; was the lack of attention Sharon gave her niece any better than Quences's excessive demands for him to excel when all the Doctor had wanted to do was what he wanted to do?

"Oh... nice to meet you," he said at last, realising that Sharon was still staring at him even as his mind raced through its various thoughts. "Sorry about that; just had an idea and had to let it run its course, you know how it is..."

"I... see," Sharon said, nodding awkwardly hat him in the manner that the Doctor had long recognises as the one delivered by humans who didn't know what you were saying and didn't want to provoke you into doing anything strange.

"Everything all right?" the Doctor asked, noting the slightly pensive expression on Sharon's face, holding up his hands reassuringly when she looked at him with a pointed stare. "Just offering my ear, that's all- bit of psychology training back at university; you can pick up a lot when you know what you're doing-; no need to reply if you don't want to."

For a while, Sharon just looked at him, am expression on her face that the Doctor had no clue how to interpret, before she finally sighed.

"It's my niece," she said at last.

"Really?" the Doctor asked looking at her in a quietly prompting manner.

"It's not that I don't care, but it's just... well, she's always been difficult," Sharon said, sighing slightly as she lowered her voice while looking at the Doctor. "I mean, I never really wanted children of my own, but I couldn't just leave my brother's daughter out on her own after... after she lost them, and then there was all this stuff a few years ago with her imaginary friend..."

"You didn't know how to relate to her," the Doctor finished, briefly finding himself recalling his own childhood; never hated, but never understood either, as Quences preferred for him to live his life according to what Quences wanted from him rather than look at what he wanted to get out of life himself, everyone else resenting the favouritism he received from the Housekeeper and never understanding why he was so relaxed and dismissive of that favour...

"She was so mature for her age already when she was arrived, it was just... it was easier to let her raise herself most of the time, and then there was work..." Sharon said, shrugging awkwardly before she trailed off and looked suspiciously at the Doctor. "Hold on; why am I even _telling _you this-?"

"I like to think that I have one of those faces that people can easily talk to," the Doctor said, smiling reassuringly at Sharon. "Don't worry, everything we've talked about here will be covered under Doctor confidentiality."

"Just 'doctor' confidentiality?" Sharon asked with a slight smile.

"You're my acquaintance, not my patient; the other type doesn't apply," the Doctor pointed out, shrugging slightly as he smiled at her. "And don't worry about your niece; children are more resilient than we think sometimes. You're there if she ever needs you; that's the important thing."

He briefly remembered that Sharon hadn't listened to her niece when Amy was telling stories about her 'Raggedy Doctor', but that was an issue that could be easily ignored; given the limited evidence that anyone else had been there, it was only natural for her to assume that he was nothing but a figment of an overactive imagination.

Deciding that it was better to leave before he pushed his luck any further, the Doctor turned around and began to walk down another isle, idly scanning the shelves for anything he might need, pushing his brief encounter with Sharon to the back of his mind and hoping that she would do the same.

He still may be relatively ignorant of where this new relationship with Amy was going to go in the end, but he was increasingly certain of one thing; she was going to be a _very _interesting permanent companion when the time came for her them to start travelling together regularly...

* * *

><p>AN 3: Hope you liked that; coming up next, something a bit different, as the Doctor and Amy take a trip into Earth's future for Amy's summer holidays, and have to deal with a certain threat from the <em>other <em>2010 Christmas special...


	12. The Perils of Poseidon

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: A few more months skipped over; we're now mid-way through Amy's summer holidays, almost a year after the Doctor came back into her life- so around 2005 in real-world terms-, and ready for another trip in the TARDIS...

AN 2: A reference to a couple of past adventures of the Doctor's that ended in a significantly different manner here to the way it ended in canon, but the real twist at this point is what adventure the Doctor and Amy are experiencing now (Most of the key plot elements will be the same as the original story, but I'm changing a few details to make it work more as a story rather than as a game, as well as altering some points to work with my long-term plot)

The History of Paradox

"London _flooded_?" Amy said, looking at the Doctor incredulously as he casually entered the coordinates on the TARDIS console. When her summer holidays had started and her exam results had come through, the Doctor had initially insisted that she spend some time with Sharon- for some reason he was encouraging her to consider things from her aunt's point of view more than he had in the past; Amy had to admit, she'd never really considered that Aunt Sharon just hadn't known what to do with her-, but although she'd had fun on Sharon's impulsive holiday to Spain, as far as Amy was concerned, her real holiday was starting now.

She'd told Sharon that she was spending time away with a friend's family, and the Doctor had assured her that he had one of his old companions available to act as a cover story if Sharon tried to find Amy before they were ready to come back; as it was, the Doctor was planning a short hop into the future as a holiday, and then he intended to spend some time giving Amy a few crash courses in some of the skills she'd need as his companion, rather than the general knowledge lessons she'd been receiving so far.

"Global warming; it's never going to get as bad as your lot seem to think it will, but it will get _pretty _bad before you manage to repair the worst of the damage done to the environment," the Doctor explained, as he worked away at the TARDIS controls. "I just thought you'd appreciate the chance to confirm that it's never going to turn out as badly as your scientists assume it will; besides, it's a fascinating area to visit, with all the benefits of exploring a new world without going off-world."

"OK, fair enough," Amy said, before she smiled thoughtfully as another thought occurred to her. "By the way... why was it so important for us to leave now?"

"Because I'm on Earth," the Doctor explained, without bothering to ask how she'd guessed that he had an ulterior motive; he thought that he'd concealed his slight apprehension about the upcoming potential cross-temporal situation rather well, but evidently Amy had seen through it nevertheless.

That was one benefit of spending this much time with a younger companion as she developed; she found it easier to see, predict, and understand his 'quirks'.

"But you're already-" Amy began, her initial pointed stare being replaced with confusion.

"A _younger _me will be on Earth for the next couple of days," the Doctor explained, shrugging slightly as he looked at Amy. "We'd be somewhat distantly removed from him, of course- I'll be in London dealing with an invasion by sentient plastic; I hadn't even _heard _of Leadworth by that point in my life-, but I'd rather not be on Earth at the same time as him in such relatively close proximity; things might get... complicated, shall we say?"

"We're going to be invaded by sentient _plastic_?" Amy repeated.

"Well, _semi _-sentient plastic- it's animated by an alien intelligence from the universe that existed before this one; it's a long story-, but the point is that I've already dealt with it and I don't want to run the risk of attracting the attention of that thing when it should be focused on me, so a trip seemed like the best way of dealing with the problem," the Doctor explained.

Even as he spoke, however, the Doctor knew that the story he was telling Amy was only a part of it.

In reality, while he did want to leave to limit the risk of more than one version of himself being on the same planet at the same time, he knew that he was deliberately exaggerating the risks to himself; he'd visited Earth so often that it would be hard to find a time period where he _wasn't _on the planet at some point or another, and there had been that whole incident with the Vore while Amy was away (One reason he'd discreetly provided Sharon with information about Spain as a holiday destination was that the Vore hadn't been in that part of the world that much during their attack; they seemed to prefer less equatorial climates in their initial assault) that his eighth self had dealt with.

His reasons for wanting to leave now were simple; he wanted to limit the possibility that he'd give into the temptation of going to look for his ninth self's temporary companion during or after that fight against the Autons and disrupt her life any more than he already had.

_Rose Tyler_... the kind, happy, blonde girl who'd saved him from the Autons at the crucial last minute before the Nestene Consciousness would have devoured him...

In a kinder universe, he might have asked her to travel with him- she'd had the right spirit, and she'd definitely had the potential to be more that he had always looked for in his companions when he had the chance to choose them; the possibility to be more than what real life allowed her to be-, but with the Faction on his tale, and his meeting her so shortly after that close call with Marnal and the Vore, he couldn't risk bringing someone so comparatively innocent into his life and force her to confront everything he had to deal with now that the Faction were so powerful.

He was doing everything he could to prepare Amy for what she would have to face if she began to travel with him, but even then the fact that she had undoubtedly already attracted the Faction's attention by her mere existence- the implications of the crack in her wall, his encounter with Prisoner Zero, and so many other factors- was one of the main reasons he was staying in her life; unlike with Anji, Trix, Rose, Martha or Donna- the most obvious potential companions he'd encountered since he lost Fitz and Compassion after everything fell apart-, the Faction _already _knew about Amy...

"Anyway," he said, smiling as he set the final coordinates, taking his mind off that dark train of thought as he resumed his original talk, "I just think that London at this time period is exactly what we need; very quiet, peaceful, and perfectly safe."

As the TARDIS continued towards its destination, the Doctor briefly noted a slight bump as the ship hit some minor distortion in the vortex, but he dismissed it as soon as it had passed him by; with the vortex in its current state with the Faction's manipulations- no matter how limited they might still be, regardless of the Time Lords' presence in the universe-, the occasional bit of turbulence was to be expected, and it wasn't even anything serious enough for Amy to notice a difference in how the TARDIS usually travelled...

After a few more moments of travel, the time rotor came to a halt as the TARDIS solidified, leaving the Doctor smiling over at Amy as he took a last glance at the ship's coordinates- a slight trace of pan-dimensional energy in the area, but nothing that couldn't be accounted for by residual energy spread out by the TARDIS after it encountered whatever it ran into- before activating the door controls.

"Here we are," he said, smiling as he led Amy into the TARDIS's new landing area; he was slightly disappointed to note that it just seemed to be a storeroom, but at least it was an area where nobody would particularly question the presence of another box if they found it while he and Amy were exploring. "London after the Great Flood of the twenty-third century."

As he walked into the corridor connecting the storage room to the rest of the underwater facility where they were currently located, he smiled as he took in the sight of the world on the other side of the large glass tunnel they were standing in; a vast, brilliant blue ocean, a whole other world that could be found on Earth without even needing to leave the planet's atmosphere, free to be explored and witnessed by all in this era in a manner that would been impossible in the past...

Earth might have lost the chance to explore Ockora through the impulsive actions of its military leaders, but Earth's own oceans still had a beauty that few other planets could match...

Hearing a loud roar, the Doctor glanced upwards, and mentally cursed at the sight of a creature that resembled a massive two-tailed shark with armoured plates more than anything else.

The floods had thrown up a few evolutionary quirks as new forms of energy were used on the bottom of the seabed, but if that wasn't a Zaralok he'd forgotten more about galactic marine biology than he thought.

Of course, even if he was right about its species, that _did _raise the question of what it was doing on Earth at this time; the last time he checked, no alien species had ever even bothered to try and relocate a Zaralok, and that was without taking the fact that Earth just hadn't reached that far into space at this point in its history yet...

"Oh no..." he said, as the shark turned around and began to charge towards the tunnel, striking the glass and leaving a significant crack before he could do more than take in its presence.

"It's coming at us again!" Amy said, looking up at the terrifying sight of the Zaralok as it swam up and turned around to charge towards the tunnel again.

"That glass won't take much more punishment," the Doctor said, his gaze quickly shifting to the door at the other end of the corridor; heading back to the TARDIS might be safer, but right now they needed to find out what had brought that Zaralok here, and he had little faith in his ability to make short hops in the TARDIS with the pan-dimensional energy he'd detected in the vicinity disrupting his sensors, which meant that getting into the main area of the city was their best bet.

As the Zaralok struck the tunnel again, the glass cracked and water began to leak in, leaving the Doctor with no other choice than to pull out the sonic screwdriver and open the door as fast as possible, his ever-useful tool cycling through combinations as quickly as possible.

"_Doctor_!" Amy said, as the Zaralok crashed into another window, creating even further cracks as water began to leak down into the tunnel, cracks spreading ever further as the water pressure increased.

"Quick!" the Doctor said, the door opening as he reached out and grabbed Amy's arm, hauling her into the relatively greater security of a sealed junction terminal as the glass broke, the door slamming shut behind them just before the water could reach them. For a moment, as he slumped down against the door, he exchanged relieved smiles with Amy at their sudden victory over the monstrous shark that had so nearly made them dinner, but then he turned around and his smile faltered.

"Oh, that is not good..." he said, taking in the sight behind him as the Zaralok attempted to chew at the now-empty tunnel, clearly looking for the food that had so recently been inside the tunnel.

"What?" Amy asked, looking inquiringly at him.

"The tunnel," the Doctor explained, indicating the tunnel behind them with an apologetic smile. "I'm afraid it isn't there any more, which means..."

"We can't get back to the TARDIS," Amy finished for him, a slight frown on her face at the thought before she stood up and looked at the area around them with a smile. "So... what is this place?"

"Sub-aquatic community," the Doctor said, walking up to the end of their current tunnel where it branched off into a T-shape, two other tunnels leading away from it. "Isn't it amazing? When the oceans rose, seventy-five percent of Earth's landmass drowned, and humanity built its own new islands and moved on to the bottom of the ocean to farm and mine for minerals." He glanced back at Amy with a proud smile. "You're a resourceful lot, you humans, that's why I like you; you'll move in anywhere... a bit like hermit crabs."

"Crabs," Amy repeated, looking sceptically at him; judging by the frown on her face, his attempt to distract both of them from the thought that they couldn't get back home right now wasn't working. "Yeah, thanks a lot."

"Look at this," the Doctor said, trying to focus on the positives as he examined a map at the end of their new tunnel, indicating a larger building a few tunnels away from their current location. "Poseidon Eight, that's the closest; come on, be rude not to say hello."

A more detailed analysis of the map was all that the Doctor needed to confirm that there were actually several routes they could take to Poseidon Eight; each major junction point had at least two tunnels running in the same direction, with the tunnels all converging on Poseidon Eight so long as they kept on heading for the large building at the end of the current route.

"Well then," he said, smiling as he turned to hurry down the right route- they weren't going to get anywhere by hanging around, one tunnel seemed the same as another, and he didn't want to spend too long in one place in case the Zaralok noticed them and tried to attack again-, "let's be off."

"Right behind you," Amy said, smiling as she hurried after him, her usual enthusiasm unhindered by the complications of their current situation (That was one thing the Doctor particularly appreciated about Amy; her natural reaction to him unintentionally leaving her alone for so long aside, she never seemed to let anything dampen her enthusiasm for discovery for long).

As they ran through a small storeroom, the Doctor briefly noted the large boxes in each room, but focused on his final destination; with something strange taking place in this city, casual investigation would have to wait until later. He noticed a few side-doors as they ran through some of the tunnel junction areas, but his focus remained on their target of Poseidon Eight, the Time Lord repressing his usual curiosity about his surroundings in favour of tackling the more immediate mystery he'd already discovered. The tunnels were relatively long, and he had to use the screwdriver to open one or two doors, but they managed to stay ahead of the orbiting Zaralok long enough to reach the final tunnel before their destination, a large metal door at the other end.

"What is that thing?" Amy asked, looking anxiously back at the Zaralok as it swam towards the tunnel they were standing in while standing in front of the final door; they'd been able to evade the shark by staying on the move before now, but their prolonged stillness at this point was definitely going to work against them. "It's not like any shark _I_ ever saw."

"Of course not," the Doctor said, continuing to speak even as the Zaralok rammed into the glass tunnel right next to their location; this door was proving to be a lot more stubborn than some of the doors he'd encountered on the way here. "It's not a shark, and it's not from Earth-"

Further conversation was halted as the door opened before the Doctor could do more than pull out his sonic screwdriver, revealing a young man about the Doctor's physical age dressed in a blue top and brown trousers with some kind of elaborate collar around his neck.

"Quick!" he said, looking urgently at them. "Inside!"

Immediately, the Doctor and Amy ran through the door, leaving it to be sealed behind them as the Zaralok rammed the glass again; the Doctor could only hope that it wouldn't keep ramming the tunnel after that first attack now that there was nobody in there, or they'd _really _be in trouble...

"The Doctor; Amy," he said, indicating himself and his friend as he looked at the other man with a smile. "You?"

"Martin Flannigan," the other man replied, looking curiously between the two new arrivals. "Doctor? Then there's a hospital ship up top? You came down in a Bathysphere?"

"Bathysphere?" Amy asked in confusion. "Is that a twenty-third century submarine?"

"She's more experienced than she looks, but she's still getting used to the pressure down here," the Doctor said as Flannigan looked curiously at Amy, evidently noticing her age; the Doctor just hoped that his spur-of-the-moment explanation would account for the most obvious questions that Flannigan might have about her presence.

"Oswald must have gotten an SOS out," Flannigan said, looking hopefully at the Doctor; evidently, the current crisis was serious enough that he was content to accept the Doctor's admittedly weak explanation for Amy's presence for the moment. "Maybe Jones'll let me into Poseidon, now that there's medical help."

"Who needs medical help?" the Doctor asked, already hoping that Amy would be all right; he'd given her the standard universal vaccine he gave all of his companions shortly after she'd entered the TARDIS for the first time, but that didn't mean that particularly virulent diseases couldn't affect her...

"The sickness!" Flannigan said urgently. "It's taken everyone on the base! Oswald has put the place on lockdown; that's why Jones won't let me in. I was working a harvester out on the prairie when that... creature attacked us; killed Pat, the base leader."

For a moment, Flannigan seemed to break down, his head lowering and his voice trembling, but he seemed to collect himself as he finished his sentence. "I'm the only survivor... and then Jones won't let me in because of the quarantine! The creature had knocked out their communications, and I've been stuck here for two days!"

"What kind of idiot is this 'Jones'?" Amy asked, looking incredulously at Flannigan.

"It's a computer," Flannigan said, glaring scornfully at the large six-sided object in the centre of the room (The Doctor momentarily wondered if he should be concerned that the design reminded him briefly of the TARDIS, given the glowing blue column emerging from the top and the multitude of lights blinking around it, but quickly pushed that thought aside; it was probably just a coincidence).

"Hello, Jones," he said, walking up to a large circular attachment on the side of the console that gave the impression of being a microphone/speaker system. "I'm the Doctor. Now, what's all this about you not letting in my good friend Martin Flannigan? Just let us in, there's a good... computer."

"_Poseidon community is on lockdown_," Jones replied, in an abrupt tone of voice that sounded slightly female despite its obviously artificial nature. "_Quarantine must be maintained to safeguard the staff on Poseidon_."

"You're a class-fourteen with nexus prime as standard and they've got you guarding the doors?" the Doctor said, eyes widening in slight surprise as he recognised Jones's design at last. "It's hardly worthy of your talents; I bet you could run this whole base if they let you."

"_I do have considerable skills which are not currently being utilised_," Jones replied, sounding almost frustrated at that fact.

"It's rubbish being clever sometimes, isn't it, Jones?" the Doctor said, smiling sympathetically at the computer. "You end up looking for impossible things to do just for the challenge... you've done that, haven't you?"

"_Well... the other day I solved the Angeladies Equation, just to see if I could_," Jones said, its mechanised voice managing to sound slightly proud and sheepish at the same time

"That's brilliant!" the Doctor said, curious about the computer's solution even if it he wasn't trying to bond with it. "Did you use the Kessler Chart?"

"_No; it doesn't allow for the four-dimensional drift_," Jones clarified. "_I came up with a new paradigm; it took fourteen hours_."

"Ah yes, well done," the Doctor said, before his expression shifted into a glare as he stared at the microphone/speaker. "But, even with all that processing power, you haven't noticed that you're _not _safeguarding the staff."

"_What do you mean_?" Jones asked.

"Well, Martin's not safe; he'll starve to death," the Doctor said, his hands nonchalantly behind his back as he addressed the machine before him. "I'm a doctor, and I can cure everyone in that base; keep me out here and they'll all die, and I bet you're fitted with standard nexus prime laws preventing you from injuring a human or allowing a human being to come to harm through inaction?"

"_But Poseidon community is on lockdown_," Jones said, falling back on its core orders when faced with an uncertain situation. "_I cannot open this door_."

"How about a compromise?" the Doctor asked, changing tactics through knowledge of his own long experience with machines. "If you release the manual override, then _we _will open the door, not you."

"_And I wouldn't have to actually open the door myself_?" Jones asked

"No breach of your programming at all; scout's honour," the Doctor said, smiling reassuringly at the computer. "How about it; does that work for you?"

"_It's an acceptable, logical solution_," Jones replied. "_Releasing manual override now_."

As he noticed the relevant console light up off to Jones's right, the Doctor hurried over and activated the controls, opening the large door at the back of the room and revealing the elevator on the other side.

"Open Sesame!" the Doctor grinned, looking in approval at the lift before he turned back to the computer. "Thanks for your help, Jones."

"_It's been a relief to talk to someone who understands me, Doctor_," Jones replied, prompting the Doctor's eyes to widen in surprise as he processed Jones's words (He thought he saw Amy glare slightly as the computer spoke, but the expression passed so quickly that he couldn't be sure it was ever there).

"Uh... right," he said, turning around to head for the now-accessible lift with Amy and Martin, the doors closing behind them as they began their descent towards the main facility in relative silence; Amy was excited at the possibility of what would be waiting for them at the bottom, the Doctor was going over possible explanations for the anomalies they'd encountered so far, and Martin seemed to just be stuck for anything to say to the two new arrivals.

Arriving at the bottom of the shaft after a few moments, the lift doors opened out onto a large room, with circular tables surrounding four large columns stretching up to the roof, and various lights spread out between the columns that hinted at the local season even without the large Santa in one corner. A walkway around the side seemed to lead up to a central observation area with a main control panel above the lift entrance, but as far as the Doctor and Amy could see the only people in the room when they arrived were a woman about Martin's age with Asian features dressed in a green shirt and cap, and an older man with short hair dressed in a similar outfit to Martin's own clothing.

"Oswald!" Martin said, grinning broadly at the two residents. "Dana!"

"Martin!" the woman said, smiling as she turned to look at him.

"We thought you'd been killed!" the other man said, before his momentary enthusiasm faltered and his expression became more sullen. "Merry Christmas, for what it's worth."

Amy opened her mouth as though about to say something, but a warning hand on the Doctor's shoulder prompted her to remain quiet; he might have arrived a few months later than he'd been aiming for, but there was no point making the anomaly that obvious.

"When you put Poseidon into quarantine, Jones wouldn't let Martin through, but that's going to happen if you have a class fourteen computer system with a nexus prime processor doing the work of a 1984 PC," the Doctor said, smiling casually at Oswald; as always, he was going to operate on the assumption that acting like he was someone in authority would stop anyone asking what he was doing there. "It's like putting Einstein in charge of a supermarket check-out; going to get grumpy and play-"

"Who _are _you?" Oswald asked, looking pointedly at the Doctor.

"He's a doctor," Martin said, pointing upwards towards the ocean surface. "There's a hospital ship up top-"

"There isn't a hospital ship, actually," the Doctor corrected before he smiled reassuringly at Oswald. "You don't _need _any hospital ship; you've got me! You couldn't wish for a better Christmas present."

"I'm Amy," the younger girl added, smiling slightly at the group of three as their attention turned to the young girl standing beside the Doctor. "His... assistant."

"You're not looking too good-" the Doctor began to say, reaching up to touch Oswald's cheek as he noted the pale colour of Oswald's skin.

"Get away from me," Oswald practically growled, brushing the Doctor's hand aside before he could make contact.

"Oswald," Dana said, her tone a calming one that suggested she was used to being the diplomatic one in these situations. "He's just trying to help."

"Bingo!" the Doctor said, pointing at her with a grin. "Well-observed! Who are you?"

"Dana Tanaka," Dana replied. "I'm the Poseidon medic. The sickness kills off the red blood cells; it doesn't respond to anything. We've confined non-essential crew to their quarters."

"If he's not from the hospital ship, where did he come from?" Oswald asked, looking suspiciously at the Doctor. "There's too much weird stuff going on around here..."

Before the Doctor could think of an appropriate response to Oswald's question, the room around them suddenly went dark, followed by the red emergency lighting turning on.

"It's the lights!" Martin said, the Poseidon crewmembers looking anxiously at their surroundings.

"What are you scared of?" the Doctor asked, before a horrible thought occurred to him. "It's not just the sickness, is it?"

"They hide in the shadows," Dana said, a slight tremor in her voice as she spoke. "They come in the dark..."

"What does?" Amy asked, the teenage girl moving closer to the Doctor as he wrapped his arm around her shoulders, already reaching into his pocket for the sonic screwdriver with the other hand. Before anyone could answer Amy's question, there was a few short seconds of total darkness accompanied by the sound of something being apparently torn apart, before the red emergency lighting returned, revealing the skeleton of what had been Martin Flannigan moments ago.

"The Vashta Nerada," the Doctor said grimly, staring at the skeleton as he recalled his last encounter with the undefeatable living shadows; he still didn't know who or what River Song was that he would have gone to those kind of lengths to save her in the screwdriver, or how she'd known _that _secret...

"Martin!" Dana said, staring in horror at the skeleton that had been a living being mere moments ago.

"What... what happened to him?" Amy asked, staring up at the Doctor in terror.

"Vashta Nerada," the Doctor explained. "Carnivorous photo-organisms that live in the dark like schools of piranha fish swimming in the shadows; the reason every culture in the universe has a fear of the dark."

"I am _never _turning the lights off again, _ever_," Amy said shaking her head as she stared at the skeleton (Even if he hated that she had to see something like this, the Doctor had to give her credit for holding herself together even in the face of her first dead body, particularly one that had been stripped clean in such a thorough manner).

"The Vashta Nerada on Earth are usually timid; feed on roadkill," the Doctor said, indicating Martin's corpse as he turned over this new evidence in his mind. "But this, down here, this is something else; this is alien."

"It started with the flash..." Dana said reflectively

"Flash?" the Doctor asked, looking sharply over at the medic. "What flash?"

"Two days ago; lit up the ocean bed," Dana replied, pointing at one of the nearby windows displaying the surrounding ocean. "The sickness, that creature, the shadows... it all started then."

"We have to evacuate this base," Oswald said.

"Good plan, bad idea," the Doctor said, clapping his hands together as he looked criticall at Oswald. "Life-pods, lots of dark corners; your people will be dead before they've reached the surface."

"We're on emergency lighting," Oswald practically growled in response. "It won't last much longer; I've got to get everybody off Poseidon!"

"_Or _I fix the generator," the Doctor corrected, looking down at his companion with a smile. "Come on, Amy! You two, stay out of the shadows and forget about the lifepods; we'll be back soon."

As he and Amy headed for the lift, the Doctor's arm around his companion while the other held the sonic screwdriver, ready to activate it the moment the lights looked like they were going to dim again, the Doctor could only hope that his statement would prove to be accurate; the Vashta Nerada might not be particularly intelligent, but that didn't mean that they were to be underestimated...

* * *

><p>AN 3: So, what does everyone think of my take on 'Shadows of the Vashta Nerada' so far? Might seem the same so far, but I DO have plans to change certain details later on, I assure you...<p>

Oh, and to those who wonder at the reference to River Song, that is _not _a mistake; for the moment, let me just remind you that time travel is VERY complicated and assure you that I have an explanation for that anomaly...


	13. Death in the Dark

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Hope this works; the corridor sequences weren't easy...

The History of Paradox

As he walked out of the lift, the Doctor's eyes immediately noted the darkness of the corridor outside Jones's chamber; this room might be relatively well-illuminated- presumably the base designers had created Jones with an emergency power supply so that she couldn't shut down and put the rest of the base at risk-, but once they stepped outside the corridor they were taking a risk at every step in the darkness.

"We can get to the generator through the corridors, but they're too dark," the Doctor said, partly thinking out loud and partly explaining the situation to Amy as he pulled out the sonic screwdriver and aimed it at a light switch near the door. "I'm going to need to give the emergency light switches a boost with this; hopefully we can divert enough power to override the Vashta Nerada's control."

As he aimed the screwdriver at the light, he smiled in approval at the sight of the corridors' illumination shifting from the dim red of the original emergency lighting to a steadies, brighter light; it didn't remain illuminated for long, but it came back on after a few moments, giving the Doctor the chance to wait for another few moments before the lights came back on again.

"_Run_!" he said, taking Amy's hand and hurrying down the corridor, the lights flickering as they reached the end of the corridor and found themselves in the more illuminated terminal.

"Hold on," Amy asked, looking between the tunnel they'd just passed through and their current location, "how come-?"

"The tunnels possess less electricity as they're essentially simpler constructs and the designers wanted to limit the possibility of electrocution-related accidents; these terminals are more heavily wired and therefore make it more difficult for the Vashta Nerada to disrupt the lighting in them as they take priority for the generator when it's in this kind of condition," the Doctor explained, quickly glancing at the map in front of him before he smiled and turned back to look at Amy. "Come on then, Pond; generator room's this way!"

Turning to look at another darkened corridor, the Doctor suddenly reached into his jacket pocket and pulled what Amy could only think of as a large light-stick out of his pocket, holding it up in front of him as he looked at her with a smile.

"Just stay close, hold on, and don't stop running," he said, taking her hand and holding her close to him before they started to run down the corridor, the light-stick held out in front of them as they ran.

"Why didn't you use that earlier?" Amy asked as they hurried through another terminal area.

"Forgot about it, to be honest," the Doctor replied, shrugging apologetically before they hurried through another tunnel. "So many things in these pockets these days; it's hard to keep track of what's in what..."

After a quick race through a storeroom and another corridor- the lightstick was efficient, but the Doctor wasn't going to underestimate the Vashta Nerada after what they'd done the last time he'd fought them-, the Doctor and Amy found themselves in the side corridor that the previously-consulted map had identified as the location of the generator.

"Got here at last," the Doctor said, smiling as he slipped the lightstick back into his pocket- it wasn't needed any more, given how brightly the corridor before them was illuminated, and draining its power wouldn't accomplish anything- and walked casually through the tunnel towards the room. "And good old Jones; she's opened the airlock to the generator!"

"So..." Amy asked, looking uncertainly at the Doctor as they walked down the corridor into the generator room, revealing a large but dark room at the end of the tunnel, "what do we do now? Add money to the meter?"

"I can do better than that," the Doctor said, smiling in approval of Amy's attempt at humour despite the grim turn of their attempted holiday as he pulled out the sonic screwdriver and aiming it at the ceiling. "Let there be light!"

As the screwdriver reached the temporarily-dormant lights in the upper level, the generator room was revealed. It was a fundamentally basic structure, consisting merely of the large generator and a few boxes scattered around that presumably contained spare parts in the event of an emergency, as well as an upper walkway that would presumably allow for relevant maintenance to be performed on the generator if it was needed.

"Right then," the Doctor said, clapping his hands together with a smile, "let's get to work."

"Doctor," Amy asked, as another thought occurred to her, "even if we get the generator back up, what about the TARDIS?"

"She'll be all right; that part of the tunnel was sealed off," the Doctor said, casually scanning the surroundings with the screwdriver; no harm in making sure if there was anything else around here that could have affected the generator, after all.

"Yes, but there's still a ton of ocean between us and it," Amy pointed out

"We'll cross that bridge- or flooded tunnel- when we get to it," the Doctor said, tucking the screwdriver away in his pocket as he turned around to take a better look at the generator, only for his eyes to widen at the sight in front of him; a skeleton, dressed in an orange diving-suit and a helmet illuminated by an unspecified green light source, looking at them in a malevolent manner (Although the Doctor had to wonder if it was possible for a skeleton to look anything _but _menacing; the imagery it created alone was never exactly encouraging).

"Oh," the Doctor said, stuck for anything else to say at this sight. "Hello, sailor."

"Doctor, it's alive," Amy said, her tone obviously apprehensive as the skeleton began to advance towards them.

"The Vashta Nerada are animating it," the Doctor said, only to turn around and find himself staring at another Vashta-animated suit.

"Don't let it touch you," the Doctor said, taking Amy's hand and moving backwards as quickly as possible; the Vashta Nerada should be limited to a more basic intelligence without the memory-recorders of the spacesuits he'd encountered in the Library to draw on, but that only gave them a limited advantage given how dangerous they were. "Don't let _any _of them touch you!"

With departing from the generator room not an option given their need to fix the generator, the Doctor turned around and hurried over to a nearby ladder leading to the upper walkway; if these Vashta Nerada were anything like the last ones he'd encountered, he was willing to bet that they'd lack sufficiently fine motor control to use the fingers of their new 'bodies'.

As he clambered up the ladder, Amy just ahead of him, he risked a brief glance down, and smiled in satisfaction at the sight of the suits staring at the ladder in a manner that could have been best described as lost despite their lack of facial expressions. As he and Amy reached the top of the ladder, the suits started to walk around once more; evidently, as with most predators, when the prey wasn't immediately present they focused on the present rather than planning for the future or reflecting on the past.

"OK, we're safe now," Amy said, looking curiously at the Doctor. "So... what now? Repair the generator from here?"

"Unlikely," the Doctor replied, indicating a pair of damaged panels on the lower level that they'd just vacated; he wished that he could sound more encouraging, but if Amy had proven anything during their reunion and the subsequent confrontation with Prisoner Zero, it was that she was good under pressure if given the chance (And he was _not _going to think about how much she'd grown since then; she might have hit a growth spurt, but... she wasn't ready to travel with him full-time yet!). "From what I saw, the damage is focused on that area down there, and I don't know enough about this model of generator to feel comfortable re-wiring it anywhere else, particularly not in our current location..."

"What; worried you'll damage something holding the tunnels together?" Amy asked, an awkward smile on her face that made it clear that she knew she was guessing wrong but didn't want to voice the worst-case scenario.

"More like I'll damage whatever's keeping the remaining lights on," the Doctor replied, before he sighed and looked at the situation below them as the Vashta-inhabited suits walked around the generator, now apparently 'on the prowl' for further prey. "Still, we need to deal with the problem at hand; we can't go down there with those suits active, but we _need_ to get down there to repair the generator..."

"You said that the... dark things were controlling the suits?" Amy asked.

"The Vashta Nerada, and yes," the Doctor confirmed.

"So... what if you turned up the lights?" Amy asked.

For a moment, the Doctor was about to explain why he couldn't- with the generator in its current condition, he'd probably burn the lights out if he tried to turn the lights up-, but then he remembered the object in his pocket and snapped his fingers before he pulled out the lightstick and began to hurry along the gangwalk, reaching a point at the end of the room where the gangwalk ran directly over the generator, leaving the path below them fully exposed. As the Vashta-inhabited suits passed by underneath the Doctor, he aimed the sonic screwdriver at the lightstick and turned the stick up to full power before dropping it towards the two suits, the sheer intensity of the light causing the suits to collapse before they'd even fully registered what had just happened.

"Done it!" he said, smiling as he hurried over to another nearby ladder and practically slid down it to return to the lower level. Picking up the lightstick, his smile faltered as he noticed its blackened condition- his last little stunt had clearly burnt it out-, but he pushed that issue aside to focus on what was important; the suits were down, and that was the main thing.

"Are they dead?" Amy asked, looking apprehensively at the suits as she walked over to stand behind him.

"They were already dead," the Doctor replied, his tone grim as he studied the bodies before them. "The Vashta Nerada just hadn't done with them yet..."

As he stared grimly at the sight before him- victims reanimated by their killers; was there ever a greater crime?-, his attention was caught by something else on the suit.

"Hello..." he said, reaching over to pick a small device of the belt of the diving-suit. "This status chip indicates dangerous levels of radiation... and it's been activated."

"Radiation?" Amy repeated, looking at him in shock. "As in-"

"It's not here now- I would have detected anything that would be _immediately _dangerous to us-, but we probably shouldn't stick around longer than we have to," the Doctor said, standing back up and hurrying back to the front of the generator, where he quickly used the screwdriver to remove the remaining pieces of the damaged panels.

"Any chance you could hurry up before the Vashtas hear the dinner-bell?" Amy asked, looking apprehensively around her; the lights in the tunnel just outside the generator room were already looking significantly dimmer, and she hadn't exactly been entirely comfortable ever since seeing Martin's skeleton.

"Good point; come on!" the Doctor said, hurrying back around to the front of the generator, opening the front hatch and quickly taking in the damage before him. It wasn't as bad as it could have been- the Vashta might be dangerous, but they were still only highly intelligent animals under more conventional circumstances-, but there were still a few loose wires that he'd have to re-solder. Modifying the sonic screwdriver to the appropriate setting, he quickly extended the severed wires to the point where they could re-connect with their other end, but a few moments' waiting and the lack of reaction confirmed that their work wasn't quite done yet.

"Mmm... generator's still not working properly," he mused, glancing over a basic diagram of the generator close to the panel he was working on. "Must be something blocking the vents... I'll keep working on it here; you head up the corridor and find the vent control switch."

"Find a switch?" Amy asked, looking at her friend in surprise. "In the _dark_?"

"Just take this and keep an eye on the lights," the Doctor said, tossing the lightstick towards her as he studied the control panel. "I'll keep an eye on things here and try to keep the lights going in the right direction; good luck... flicking that switch."

* * *

><p>"Right," Amy said, nodding resolutely as she turned to look at the corridor behind her.<p>

This wasn't the way she'd wanted to help save the day in her travels with the Doctor- particularly not after the stories she'd heard about some of the things he'd encountered-, but as a first crisis, she supposed it was a good way to start experiencing life with the Doctor in _his _world rather than hers...

"Just stay on the bright bits..." she said, taking a breath as she waited at the end of the corridor before she ran along the corridor as the emergency lights reached her end, the lightstick clutched in her hands just in case they shut down on her. Running from one junction to another, the next relevant corridor being illuminated for her based on what she could only assume was the Doctor's work, Amy finally found herself walking into a room with four large fans on both walls, a prominent switch on a large device at the other end of the room from the corridor.

"Huh," she said, stuck for anything else she could do as she walked up to the switch, flicking it with a slight shrug; after the danger posed by the Vashta Nerada, that really felt almost too simple...

"That sounds better," she said, turning around to take in the room around her as the fans began to spring into life. "Hopefully that generator will spring to life now..."

Glancing out at the corridor, Amy tried not to feel too anxious at the sight of a still-darkened corridor; it was possible that the Doctor hadn't finished what he was doing at the generator. Taking a deep breath, she ran back along the corridors, the lightstick still held out in front of her in case she missed the pattern of the lights, until she finally reached the generator room once again.

"That did the trick, Amy," the Doctor said, glancing back at her with a brief smile as he adjusted the wiring behind another panel. "One more poke around with these wires, and we should be sorted..."

He smiled in approval as he finished linking the last couple of wires in front of him, the generator whirring into life as he made the last connection.

"Brilliant!" he said, grinning over at her. "Well done, Engineer Pond! Now let's find out what's really going on here..."

"What do you mean, 'really'?" Amy asked, looking at him curiously.

"The sickness, the Vashta Nerada, Flipper with the big teeth out there, they're all connected," the Doctor said. "Something had to set this off for a reason..."

"It's that flash of light they all saw, isn't it?" Amy said, smiling in uncertain understanding.

"Thanks for chipping in, Amy," the Doctor said, pulling out the status chip he'd acquired from the diving-suit earlier. "Come on; Jones may know more."

"Well, at least it's brighter now," Amy said, smiling optimistically at him as they hurried back along the corridor towards the main Poseidon base.

"Quite," the Doctor said, glancing up at the Zaralok as it circled above the corridors. "Too bad that thing's still floating around..."

"Is it dangerous?" Amy asked.

"Only as dangerous as anything genetically engineered for war could be," the Doctor said, shrugging slightly. "That's the problem with war, really; it pushes scientific development forward several years, but it can turn up some very _unpleasant _developments in the process..."

Shaking it off, he smiled as he walked into Jones's control room, smiling casually at the computer as he pulled out the status chip. "Hello, Jones, me old mucker; can you have a butcher's at this for me?"

"_Certainly, Doctor_," Jones said, as the Doctor placed the chip in a small plug located underneath the speaker. "_It's a standard environment status chip, issued to all Poseidon personnel_."

For a few moments, there was nothing but a low beeping as the computer analysed the chip, until Jones spoke again. "_That's strange... I'm picking up some unknown radiation. I'm supposed to be able to identify every possible type of radiation. My sensors must be damaged_."

"No, your sensors are working perfectly, Jones," the Doctor said, patting the side of the console reassuringly. "You can't identify it because it's alien, and I'm fairly sure I can fix the source of it too. I need to tell the others."

"To the lift?" Amy asked with a smile.

"The lift, and the assembly hall," the Doctor confirmed, walking into the lift and pressing the relevant controls. "We have an unknown amount of time until that sickness spreads; the sooner I can make a start on a cure, the better."

Amy wasn't sure if she was just imagining it, but something about the Doctor's expression suggested that even he didn't think it was going to be that simple...

* * *

><p>AN 2: Short, but I'm hoping to include a few more divergences from canon in the next chapter...<p> 


	14. Underneath the Mask

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

The History of Paradox

"Ah, Dana," the Doctor said, smiling at the older woman reassuringly as he walked out of the lift to find her standing in the assembly hall. "Good news; I've got the generator back up and running- for the moment, anyway; what's been broken once can break again, after all-, and I've got a few ideas about how to cure that sickness you mentioned."

"You do?" Dana asked, looking at him in surprise. "But I haven't even identified the _cause_-"

"The Doctor's a genius," Amy said, smiling reassuringly at Dana. "Trust me on this; if he thinks he can cure that sickness, he'll at _least _make anyone suffering from it a lot better."

In a strange way, Amy's indirect acknowledgement of his failures made the Doctor grin all the more broadly at her; she respected that he wasn't perfect, and she _still _wanted to travel with him when she was old enough...

"I'd better explain the full details to Oswald; best to keep the commander abreast of things, after all," the Doctor said, clapping his hands together before he looked curiously at Dana. "Where is he, by the way?"

"Checking the life-pods in case we have to evacuate," Dana replied, indicating a door at the other end of the hall. "It's back that way."

"Right; lead on," the Doctor said, even as the apprehensive glance he shot at Amy was enough to convey his concerns at this latest news; why, after witnessing what the Vashta Nerada were capable of in darkness, would _anyone _bother to prepare darkened life-pods for launch?

He shook those thoughts aside as Dana took them through the large doors at the back of the room, past a series of lockers, and into a side room with at least four life-pods present

"Oswald!" Dana said, looking at the base commander as Oswald climbed down from examining one of the life-pods. "The Doctor thinks he can synthesise a cure for the sickness!"

"Poseidon is guaranteed to have what I need," the Doctor said, looking at Oswald with a positive smile on his face. "Sea sprouts, brine oil, sticky mushrooms, those things are always growing in some damp corner of an undersea base like this."

"This is a joke, right?" Oswald said, looking sceptically at the Doctor.

"Well, you might use brine oil to keep your machines going, but it's also full of iodine," the Doctor clarified.

"They need the access codes to get on to the agricultural sectors," Dana explained, evidently anticipating the Doctor's next necessity before he could ask for it himself.

"And by the way," the Doctor added, looking more sternly at Oswald, "I thought I told you; trying to get your people off Poseidon in life-pods will just get them killed."

"So I just twiddle my thumbs while you mess around with some crack medicine?" Oswald countered, glaring back at the Time Lord.

"If you really want to save your people, you'll listen to the Doctor," Amy said, staring firmly at the older man.

"And let you go mushroom-picking to get eaten by those things in the shadows?" Oswald said, shaking his head firmly. "No way! Enough people have died! No-one else, Doctor! It's too dangerous! We've got one chance, and it's these pods! And this is a restricted area; get out!"

Glancing over at Amy, the Doctor placed a calming hand on her shoulder- he appreciated her indignant glare at Oswald on his behalf, but it wasn't going to get them anywhere- and led her out of the room.

"I'm... sorry about him," Dana said, looking apologetically at them as they walked away from the pods and into a room that looked like the facility's laboratory, filled with all kinds of devices that looked like enlarged microscopes at a casual glance, with a white room that looked like a medical bay off to the side with various beds around the walls. "Oswald is a good man, but so many people have died... he's only trying to do what he thinks is right."

"Too bad that it's the wrong thing," Amy said, glaring at the older woman. "The Doctor _needs _those access codes!"

"But Oswald's not the only one who has them, is he?" the Doctor said, looking at Dana with a thoughtful smile. "You're the chief medical officer on this base; you have to know the codes yourself..."

"I'm sorry," Dana said, looking sympathetically but firmly at the two new arrivals. "I can't give them to you."

"We fixed the generator; it must be safer out there now," the Doctor said, looking at Dana with a reassuring smile as he resisted the temptation to express his current frustration more vocally.

"We'd be taking all the risks; not you-" Amy began.

"And I'm responsible for your safety," Dana said firmly. "I can't let you go."

"I'm sure I'll find the ingredients in the storerooms out there-" the Doctor began.

"But you're not certain," Dana said, looking apologetically at the Time Lord; she evidently wanted to believe him, but was focusing on what she knew of the situation regardless. "It's too risky."

"You're not putting Oswald in danger or breaking his trust," the Doctor said, stepping forward to look more directly at Dana, an earnest expression in his eyes as he stared at her. "I know what I'm doing, and I'll take every precaution possible; this will help all of us, but you have to give me the chance to try."

"Look," Amy said, looking at Dana with the same earnest stare that she'd used to get her way so often in the past when faced with difficult teachers in the past, "I know this is all scary and confusing to you, and you think it's easier to stick with what you know, but trust me; the Doctor _can _do this. I've _seen _him do this kind of thing before, and it's worked because we gave him a chance; you just have to trust him now."

After looking solemnly at the little red-haired girl with eyes that were far too old for her face, Dana nodded.

"Fine..." she said, looking grimly at the two of them. "But be careful, and try to get back before Oswald notices."

"Thank you, Dana," the Doctor said, grinning warmly at her. "And I am always careful, and when we come back with the cure, you'll be glad we went."

"I'll enter the codes now," Dana said, turning around and walking over to a table with a speaker/microphone on it similar to the one attached to Jones, tapping a few buttons on a panel underneath the speaker.

"_Access codes accepted_," Jones's voice said. "_Security override released_."

"We're trying to do this on the _quiet_, you numpty!" Amy said, glaring at the speaker before she smiled at herself as though realising how foolish what she'd just said was.

"Come along, Pond," the Doctor said, turning around and hurrying towards the assembly room, which they quickly ran through on their way to the lift.

"So, how long have we got?" Amy asked, as they entered the lift and began their ascent.

"Oh, several minutes, I'd assume; the pods might be straightforward bits of equipment, but even if Oswald doesn't believe me about the Vashta or the Zaralok he'll want to make sure that nothing's been damaged before he launches them," the Doctor replied, before the doors opened and the two of them were in Jones's room once more. "All right, with the corridors illuminated, so long as we move quickly the Zaralok shouldn't be an issue; I'll look for the sticky mushrooms, and you check the storeroom on our right- the one on the left once you start going back towards the TARDIS, I believe- for the sea sprouts and the brine oil container; I'm fairly sure I saw some there earlier..."

"Meet back here in a few minutes?" Amy asked, smiling at her friend.

"Well, you should be here then, anyway; might take a _bit _longer to find the mushrooms," the Doctor said, shrugging briefly before he waved her along. "Just remember; keep moving!"

* * *

><p>Looking up at where the Zaralok was still swimming in the distance, Amy nodded in understanding and ran down the corridor, years of attempts to escape the taunting of other children for her 'imaginary friend' now helping her aid him in his latest task.<p>

A part of her almost couldn't believe it; she was actually helping the Doctor to _save lives_...

She knew that what she was doing was relatively minor in the grand scheme of things- finding a few things lying around the base wasn't exactly disarming the bombs or rewiring the ship's engines-, but she knew that she couldn't expect to be trusted with something that complicated this relatively early in her time with the Doctor; this was only the first time she'd actually been in this kind of position...

After a few moments of hurried searching, she found a small can containing what appeared to the oil that the Doctor had mentioned he was looking for earlier. Slipping the phial into the pocket of her blue coat, Amy hurried into another storage room where she found some large green sprouts that were almost certainly the sea sprouts the Doctor had asked her to look for. Carrying the sprouts in her arms, she hurried back towards the entrance to the Poseidon Eight base, where she found the Doctor standing with a few large sticky mushrooms clutched in his hands.

"Are those really needed?" Amy asked, looking at the mushrooms with a slight wince.

"It's all necessary, I assure you," the Doctor said, smiling reassuringly at her. "It won't exactly be pleasant, but then, medicine never does, does it? Let's just get back to the lab and work on that cure."

Stepping into the lift, the Doctor and Amy headed down to the meeting room, quickly hurrying from there into the labs.

"We've got everything," the Doctor said, indicating the ingredients in his and Amy's arms with a smile at Dana. "Everything else I need should be here already; just give me a few moments, and I should be able to put it all together."

"Right," Amy said, putting her collected items down as she indicated the door to the lab. "You get on with that; I'll just... take a look at the view."

It felt a bit awkward even as she said it, but Amy was just focusing on the facts; she couldn't help the Doctor do anything right now, and she'd been wanting to take a good look at the city anyway.

Heading over to the assembly hall, Amy climbed up the stairs to an upper level, walking up to the console room at the other end, where she could take in the sight of the city around her with a relaxed smile at the sight before her.

Even with the shark-like thing that the Doctor had called a Zaralok swimming around the city spread out before her, the sight of the glass tubes spread out between the various connecting terminals she and the Doctor had been walking through earlier, now illuminated and glowing a brilliant blue amid the fields of undersea crops, followed by the more distant sight of larger, more contained buildings that were probably living accommodations.

It might not be space travel, but for her race to have built something like this underwater- an environment that they were almost equally incapable of surviving in- was still a _very _impressive achievement...

After she'd spent a few moments taking in the sights around her, Amy turned around and headed back to the lab, grinning happily at the sight she'd just witnessed, only for her smile to falter as she returned to the lab and saw the Doctor studying the equipment in front of him; no matter how much she might want to pretend otherwise, they still had a serious problem in front of them...

"Finished," the Doctor said, holding up a glass phial with a smile as he indicated the yellow liquid within it. "One sip, and it's all sorted."

"Do I need to...?" Amy asked, indicating the phial uncertainly; she might trust the Doctor, but she wasn't that keen on drinking something like that...

"You should be fine, really; that universal vaccine I gave you earlier should take care of the most immediate consequences of the radiation, and we'll be leaving soon enough anyway," the Doctor said, reminding her of the injection he'd given her early on during their acquaintance; it had just been a quick injection, reminding Amy of the hyposprays she'd seen on _Star Trek_, but according to the Doctor it had provided her with immunity to most common diseases she'd find, both on Earth and during their travels. "Dana and everyone else here are going to need this cure more for the long-term consequences of prolonged exposure to the vortron radiation rather than anything else."

Picking up the phial, he smiled slightly at it before he walked over to the medical wing, where Dana was sitting patiently on a bed.

"Sorry," the Doctor said, holding up the glowing yellow phial, "all out of sugar lumps."

"Is that witch's brew _really _going to fix me?" Dana asked, now slightly bent over as she weakly clutched at her stomach; Amy thought she even _looked _slightly paler than she had earlier.

"You'll feel better, I promise," the Doctor said, placing the cure in Dana's hand. She stared at it for a moment, and then swallowed, it, only to gasp in disgust at the taste.

"Quite a kick, isn't it?" the Doctor said, smiling at her. "That's the sea-worm extract; unpleasant, but necessary to get the full effect."

Amy just shuddered slightly at the thought of drinking something that had come from a worm; she might be open-minded, but that was _not _a pleasant image..."

"The Doctor's Patented Vortron Radiation Elizir," the Doctor said, smiling at her. "One hundred percent effective; you may grow hair in the palm of your hands, _but_ until that happens, I need your help, Dana."

"With what?" Dana asked.

"Vortron energy only comes from some sort of dimensional vortex-" the Doctor began.

"Are you serious?" Dana asked, looking at him in confusion.

"He's serious," Amy confirmed with a brief nod.

"Just what kind of a doctor are you, _really_?" Dana asked, looking at the Doctor with sudden suspicion.

"The kind you need," the Doctor replied, leaning forward to stare at her. "And I mean _really _need, and if I can find the source of the Vortron energy I can make everything better."

"And how do we do that?" Amy asked. "I mean, if the source was close by, wouldn't we have seen it by now?"

"Does Poseidon have external scanning equipment?" the Doctor asked, turning his attention back to Dana. "By which I mean long-range scanners?"

"Of course," Dana said, leaving the lab and taking them back to the upper console that Amy had been studying earlier. As they reached the console, Dana began to search through a few controls, activating a series of remote observation posts set up around the outskirts of the Poseidon colony.

"Done," Dana said, stepping back as she finished her immediate task. "All the beacons are activated, but... what am I searching for?"

"Just give me a moment..." the Doctor said, taking up Dana's position as he entered a series of equations and information into the console at such a speed that Amy could barely follow his fingers as they danced across the console, until he stepped back with a smile.

"There we are," he said, indicating an image on the screen, which seemed to display an old military ship (Amy thought it looked like something from her time, but acknowledged that it could have been a few decades one way or the other; navy ships weren't something she paid much attention to).

"_That's_ the source of the radiation?" Dana said, looking at the screen in surprise.

"But... you said Vortron energy came from some sort of vortex," Amy said, looking at the Doctor in confusion. "That's... just a shipwreck."

"Oh, no no no no no no no no, Amy Pond," the Doctor said, looking firmly at her. "That is the shipwreck of the USS _Eldridge_."

"Is that important?" Amy asked after a moment's pause; she'd been enjoying her history lessons more lately- they were giving her a few ideas about where she might ask the Doctor to take her when they started travelling together-, but she didn't recognise that name from anything she'd been studying.

"The Philadelphia Naval Shipyard, 28th October, 1943, Project Rainbow," the Doctor elaborated. "The US Navy experimented with Einstein's Unified Field Theory to make their warships invisible; _instead_, they break the laws of transdimensional physics, open a gateway, and the _Eldridge_ travels around the world and back again in the blink of an eye, with every man on board either dying or going insane."

"So what's it doing on the seabed?" Dana asked; either her initial confusion had been put aside, or she was just so confused at this point that she had decided to just listen to the Doctor's story rather than try to argue with him.

"My people took... steps... to stop the experiment," the Doctor explained.

"Your 'people'?" Dana repeated, looking at him suspiciously.

"That's... not important right now," Amy said, looking warningly at Dana before she turned back to the Doctor. "What happened?"

"The gateway was unstable and the _Eldridge _disappeared before they could neutralise it completely," the Doctor explained.

"And now it's here and the gateway is still open?" Amy asked. "The Vashta Nerada and that... shark thing; they came through it?"

"Exactly," the Doctor said firmly, turning to look solemnly at the screen. "And we have to close it..."

The sound of machinery from another part of the building prompted the Doctor to look back, already knowing the source of the discovery and cursing this turn of events.

"He's going ahead with it," he said, unable to completely believe what he was hearing. "Those aren't going to be life-pods your crew's getting in, Dana; they're coffins. Come on, Amy; we have to stop this."

Just as he turned to walk down towards the lab, he found himself halted by the sight of Oswald standing on the stairs, a large harpoon in his hand as he aimed it at the Doctor.

"You can't interfere," he said, staring firmly at the Time Lord.

"Oswald, you can't-!" Dana began, stepping forward to try and protest, only for Oswald to turn and point the harpoon at her. Exploiting the momentary gap in Oswald's defences, the Doctor lunged desperately towards the older man, colliding with him with such force that the harpoon flew out of his grip as the two men rolled down the stairs before hitting the floor. As the Doctor leant up from his position on top of Oswald, Amy ran downstairs to join her friend, reaching the bottom just as the Doctor reached down and-

"_Oh my God_!" Dana screamed, staring in horror at the withered mass beneath what had been Oswald's face, Amy's hands pressed to her mouth in horror as she fully witnessed a face that had only ever glimpsed in her nightmares.

Even as the part of her that remembered the Doctor's advice to always take in her surroundings realised that the Doctor had pulled off the mask of Oswald's face that had been concealing the Faction agent's true appearance, the rest of her was just focused on the sheer horror of what she was witnessing in front of her.

"As sick and twisted as ever, aren't you?" the Doctor said, glaring at the thing that had been Oswald mere moments ago, one hand on his opponent's chest as he held the man down. "Tell me, was there ever a real Oswald?"

"Until a few days ago, anyway," the creature replied, seemingly smirking through its decaying lips as it looked back at the Doctor. "Oswald Fox would have made an interesting convert, but we lacked the time; it was... easier to do it this way."

"Easier for _who_?" Dana asked, anger replacing her initial shock as she walked forward to stare at the man lying beneath the Doctor. "Who _are _you?"

"Cousin Marion," the figure replied, looking at Dana with a smirk. "Of Faction Paradox."

Amy's instinctive gasp of horror prompted Cousin Marion to turn to look at her, a grin on his face that was all the more twisted for the lack of skin around it.

"Ah, Amelia Pond," he said, smirking as he looked at her. "The first of the Lost Ones..."

"You don't even _look _at her," the Doctor said, grabbing the chin of the thing that had been Oswald Fox and forcing the Cousin's eyes back on him. "What was your goal here?"

"Just a simple case of exploiting that rift to let in a few things that shouldn't be here; childishly simple situation to test a raw recruit, you know," Cousin Marion replied, smirking as he looked at the Time Lord above him. "Of course, that's bound to change once I bring you in..."

"Why do you keep doing this?" the Doctor asked, rolling his eyes in frustration. "I keep telling you all, I'm never going to _be _him any more!"

"You will eventually-" Marion began, before the Doctor leant back and punched him in the face, the force of the blow actually cracking some of the skin around his cheek as his opponent fell into unconsciousness.

"Lucky he was just a Cousin, really; if he had been anything higher we'd have _really _been in trouble," the Doctor said, standing up and flexing his hand looking over at the still-shocked Dana. "Dana, we need to tie him up and get him somewhere secure before he wakes up; whatever he was trying to accomplish, he can't do anything if he's locked away."

"But-but-but-!" Dana protested, before Amy grabbed her arm and turned the older woman around to face her.

"Look," she said, glaring at Dana, somehow managing to appear intimidating despite being approximately a head shorter than her and inwardly shaking in terror at the thought of facing the Faction, "right now, we have a deranged time-travelling voodoo cult out to destroy this base for some reason; your job is to get that _thing _that was your boss out of the way while the Doctor and I stop this whole mess, so _do it_!"

As Dana nodded and hurried off to the lockers they'd passed by earlier, Amy looked over at the Doctor.

"What now?" she asked, trying not to look at the faceless man lying on the ground; the flesh remaining on his body made the Cousin posing as Oswald more disturbing, in a strange way that she couldn't define, than the skeleton of Martin Flannigan lying a short distance away.

"The TARDIS," the Doctor said, hurrying past Amy to head back to the control console before she could ask what he meant. "Jones, show me the service system layout!"

"_Watertight service trenches run beneath Poseidon_," Jones informed the Doctor after a moment's beeping as the relevant information was retrieved. "_Although seabed tunnels connecting to your craft's sealed location have been destroyed, access is achievable_."

"Right," the Doctor said, smiling as he tapped a couple of controls and a small hatch in the floor opened up just behind the console, between it at the window, revealing various rungs leading down. "Come along, Pond; just need to help Dana lock 'Cousin Marion' up, and then it's time to be on the move."

"To the _Eldridge_?" Amy asked, glad to have something else to think about after that particular encounter.

"Precisely," the Doctor said with a resolute nod.

Amy might have just had her first encounter with the Faction in person- hearing the stories was one thing, but seeing them in person was something else entirely-, but if the Doctor wasn't going to be cowed by their presence here, then she refused to be either.

They _would _stop the Faction from exploiting the _Eldridge_'s rift...


	15. Ending the Eldridge

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Anyone seen "The Angels Take Manhattan"? Tragic ending, but an apt way to end Amy and Rory's time in the TARDIS- particularly given Amy's bond with the Doctor making it hard for him to leave her willingly- while still giving us the hope that they had a good life...

For what it's worth, I can assure that this series is not planned to end in such a manner, and I have _quite _a few adventures in mind before I reach the conclusion (Although I can't promise that Rory will feature to a significant degree).

The History of Paradox

"Do you do this often?" Amy asked, looking up at the Doctor while trying not to look at the lower part of his anatomy that circumstances demanded be in her face as they crawled through the maintenance ducts towards the TARDIS.

"What; crawl through these kind of tunnels?" the Doctor asked, pausing to look back at Amy with a brief smile before he continued walking as he talked. "It comes and goes, really. I'm willing to take all risks, but there are some periods of my life when it can be difficult; a few centuries back, I was... well, a bit larger back then."

"You were _fat_?" Amy said, looking up at the Doctor in surprise

"I had a tendency to put on weight back then; things changed over time," the Doctor said, shrugging slightly as he continued to crawl. "Anyway, this isn't the time to consider that right now; we have more immediate tasks at hand.

"Like... what the Faction are doing here?" Amy asked, deciding to tackle the most obvious question as they crawled around a corner.

"Exactly," the Doctor said. "The _Eldridge _offers a few obvious possibilities for what they're after, of course, but there has to be more to this whole mess than just trying to ensure that the _Poseidon _residents die."

"Is there a particular reason they'd want that?" Amy asked.

"I can't _think _of anything significant about _Poseidon Eight_'s role in future history, but that doesn't mean anything; you don't have to play a major role in history for your death or survival to change it," the Doctor said. "Still, with their new freedom to act, they wouldn't limit themselves to something as comparatively small as eliminating one city; they must be interested in identifying the source..."

"They want control of the _Eldridge_'s equipment?" Amy guessed. "But you said it was dangerous-!"

"Which, for the Faction, just means it's a bit more complicated than the usual method of doing things; as far as they're concerned, the rules of time travel are unimportant," the Doctor said grimly, before he smiled slightly as he reached the end of the tunnel. "Ah, here we are; just give me a moment..."

After a few seconds of fiddling with the sonic screwdriver, the Doctor opened the hatch and stepped out into the storeroom where he had left the TARDIS, smiling in satisfaction at the sight around him. "Well done, Jones."

"We're back?" Amy asked, looking at the blue box with a relieved smile as she climbed out of the tunnel after the Doctor.

"Half-way there now, anyway," the Doctor said, pulling out his key as he opened the door of the ship and walked into the box, Amy close behind him as he headed for the console. "Just got to program in the right coordinates- a quick hop to the _Eldridge _without moving anywhere in time; don't want to give the Faction time to send in a new agent- and we're set."

"Is that possible?" Amy asked, trying not to think too much about the memory of the circumstances under which she'd originally met him; he'd explained to her that the TARDIS had been malfunctioning due to damage that it had sustained shortly before they met, but he hadn't exactly told her much about his ability to handle the TARDIS on such short hops...

"With the amount of vortex radiation the _Eldridge _is generating right now, the miracle would be if I missed it," the Doctor said, smiling as he activated the relevant controls before he pulled the dematerialisation lever- Amy noticed a brief haunted expression in his eyes, but decided it wasn't something she wanted to examine too closely-, initiating the increasingly familiar wheezing, groaning sound, which repeated itself after only a few seconds of travel.

"We're there?" Amy asked, turning for the door with a brief smile.

"Hold it!" the Doctor said, pointing firmly at Amy as he spoke, prompting her to halt her approach to the door until he had finished flicking a couple of switches and smiled at her. "OK, you can go out now."

"What was that for?" Amy asked, looking at him in confusion.

"I'm fairly sure that you can't breathe underwater, Pond?" the Doctor said, grinning at her in a slightly teasing manner. "All I did there was extend the TARDIS force field to repel the water in the immediate vicinity so that we can walk through the ship without worrying about drowning."

"Oh," Amy said, suddenly ashamed that she hadn't realised that herself as the Doctor walked past her and opened the door of the ship.

"Mmm..." the Doctor said, taking a sniff of the air outside the TARDIS's doors. "Smells a bit stale, tastes of engine oil and halibut, but it'll do; come on, Amy."

Walking out of the ship, Amy told herself not to be disappointed at how relatively tame the interior was; she might be dealing with a secret government project, but it was a secret project from the 1940s...

"What was that?" she asked, as a sudden roar filled the ship.

"Ah, _there _we are," the Doctor said, glancing out of a nearby portal to see the Zaralok floating near the _Eldridge_, somehow appearing even more menacing than usual.

"That thing... followed us?" Amy asked, looking at the Doctor in confusion. "I thought it was just a shark?"

"It's possible that the Zaralok's still slightly sensitive to the temporal ripples being generated by the equipment here and the TARDIS's presence triggered a ripple effect..." the Doctor said, shrugging slightly as he looked at the creature. "Still, shouldn't be anything to worry about; he probably just doesn't want to go home where he's no longer the absolute top of the food chain."

Amy didn't want to consider the implications of that last statement too much; the idea that there was a fish out there _bigger _than what she was looking at right now...

"Come along Pond," the Doctor said, as he turned around to continue walking down the corridor. "We have to find the accelerator; it's the heart of the whole gateway."

"And... turning the accelerator off will send that thing home?" Amy asked, indicating the window as she walked after her friend.

"Him, the Vashta Nerada, and anything else that slipped through the trans-dimensional gateway, and before those lifepods are launched," the Doctor confirmed with a smile. "Shake a leg, Seaman Pond."

The walk along the corridor progressed relatively smoothly at first, with a brief dark patch easily bypassed thanks to the Doctor's lightstick without him and Amy ever being in real danger, until they found themselves at a corridor that branched off into two directions, with a locked door at one end and stairs leading down to a damaged pipe letting off a great deal of steam to block the path.

"Right..." the Doctor said, walking over to experimentally turn a wheel near the pipe. Straining against its weight, he managed to turn it far enough to turn off the steam from the valve, but he then turned to Amy with a grim expression.

"Amy," he said, still holding the wheel, "the valve won't stay closed, and I can't do anything to hold it in place for us to go past because I don't want to risk disrupting the ship's systems until we can get to the generator; you go through while I hold it."

"And... then what?" Amy asked apprehensively. "I don't know a _thing _about how to turn this kind of generator off..."

"You don't need to," the Doctor replied with a slight smile. "That door we passed earlier, at the top of the steps; if you can find a way to open it from the other side, I should be able to follow."

For a moment, Amy panicked at the thought- the idea of going _anywhere _without the Doctor in this kind of situation felt wrong in a way that she couldn't entirely define-, but she shook that aside; she couldn't travel with the Doctor and _totally _depend on him to cope with what they encountered.

"All right," she said, taking a deep breath before she hurried along the corridor in front of her, leaving the Doctor on the other side of the valve as it began to spray steam once more, leaving her and the Doctor separated. As she ran through the corridors of the ship, alone in danger for the first time that she could remember, Amy tried to focus on her destination rather than her lack of assistance, until she finally found herself facing a ladder leading up to a small porthole above her. Taking a deep breath, she climbed up to the top and opened the hatch, emerging into what appeared to be a square corridor around a central room, but pulled back into the corridor when she noticed another skeletal diving-suit walking through the corridor towards her.

For a moment, Amy could only remain pressed against the wall, her breath as low as possible as she waited for the suit to walk past, but it finally walked away from her, leaving her to hurry away from the wall to investigate the room in the middle of the corridor. Quick observation revealed that it had a large hatch in the centre that seemed to be controllable from a couple of switches on the side, as well as a couple of doors leading into the bilge-pump area from either side, but Amy's eyes widened in shock as she noticed another diving-suit opposite her current corridor, visible through a hatch in the bilge-pump.

"Oh no..." she said, suddenly pressing against a wall as she took in what she'd just seen; two Vashta-inhabited-diving-suits, on either side of her, with no source of light available to drive them out...

_Drive them out_...

Military history might not be something the Doctor was that focused on, but he'd given her a few pointers on how some vehicles were constructed, and one of them was the presence of bilge-pumps, while allowed the crew to drain off water that collected in the ship.

_If water's flushed out through that hatch_... she thought- she didn't want to risk speaking in case she attracted the creatures to her, even if she'd found sometimes that speaking aloud could help focus her thoughts when she was uncertain about something-, _maybe I can lure the divers in there_...

Turning around as the idea occurred to her, Amy found that one of the suits was already walking towards her, arms outstretched and shadows stretching out from around it, leaving her with no other option but to hurry into the bilge-pump room and hope that the creature followed her. Hurrying for the next exit, Amy yelled at the other darkness-inhabited diving suit as it came around the corner, giving it a few seconds to approach her before she turned around and ran back into the bilge-pump. Narrowly evading the shadows whirling around the suits, Amy dashed towards the other door- one suit tried to grab her, but the Doctor's theory about the Vashta Nerada's poor motor control appeared to be accurate and it timed the grab so poorly that she was able to avoid it-, dashing out of the door and slamming her hand on the control switch. Glancing back, she watched in satisfaction as the door shut behind her and the bilge-pump opened up, water briefly filling the room before both suits were sucked out of the hatch in the floor.

"_Phew_..." Amy said, slumping against the wall at the sight, relieved beyond measure at her close call...

Then it hit her.

She'd just faced death without the Doctor for the first time- OK, there'd only really been that encounter with Prisoner Zero, but that had still been dangerous-, and she'd _won_!

Grinning broadly at the thought, Amy got up and hurried over to open the hatch that the Doctor had pointed out earlier, smiling in relief as she slid the bolt away and opened the door to reveal the Doctor standing on the other side.

"_Finally_," the Doctor said, smiling at her as he walked into the chamber with her. "Thanks, Amy; I thought I was going to be stuck out there for good."

"Just until I cleared away the danger," Amy replied.

"What danger?" the Doctor said, looking sharply at her.

"Just a couple more of those Vashta-inhabited diving suits," Amy replied, indicating the bilge-pump she'd used earlier. "They must have come here to check the _Eldridge _out- maybe they found it while setting something up and Dana didn't mention it because she thought that fishy had eaten them- and been attacked by the shadows, but I managed to suck them out with that."

"Really?" the Doctor said, momentary guilt flashing across his face before he looked at her with a broader grin. "Good for you, Pond; excellent use of your environment to defuse the current threat."

"Couldn't have done it without everything you taught me," Amy said, grinning back at him warmly.

"Now to finish the job," the Doctor said, clapping his hands together as he turned to look at a ladder in one corner that Amy hadn't paid much attention to earlier. "We've got to find the accelerator and shut it down."

Climbing up the ladder, the Doctor opened the hatch above, revealing a room filled with various criss-crossing pipes, with a walkway leading up towards the top of the room and something at the centre of the equipment.

"Now we're getting somewhere," the Doctor said, grinning at the sight before them. "If I'm not much mistaken, that's the generator at the top of the room."

"And what do we do when we get there?" Amy asked.

"Well... would it be too much to ask for an 'Off' switch?" the Doctor shrugged.

"You mean you don't know?" Amy asked, her confidence suddenly dashed at this news.

"Well, this was a _top-secret _experiment that failed, Pond; people don't tend to keep records about that kind of thing," the Doctor said, before he shrugged and turned his attention back to the task before him. "Anyway, we need to get up there first... oh, and be careful; looks like the rift is playing havoc with the machinery in here."

Amy thought about asking what he meant by that, but the a sudden burst of what she could only describe as green lightning appeared on the walkway in front of them, answering her question better than the Doctor ever could.

"Oh," she said, looking apprehensively at the Doctor. "That's dangerous, huh?"

"As is _everything _here, my dear Amelia Pond," a third voice said from behind them.

"What- _Marion_?" the Doctor said, spinning around to look at the faceless Faction Cousin in shock. "How did you-?"

"Low-quality rope in storage at Poseidon Eight; a 'natural' oversight, really," Marion said, grinning maliciously at the two in front of him as he flexed his fingers in anticipation, one hand holding a blade that looked disturbingly like it was made of bone.

"Where's Dana?" Amy asked.

"Oh, she's fine; I just nipped back in time a few days and borrowed a diving suit to come here and wait for you," Marion said with a dismissive shrug. "I had to be patient, of course, but that's the advantage of being in the Faction-"

"Yes, you don't exactly need to eat because you don't exactly exist; do you ever get tired of going on about that?" the Doctor asked, glaring at him. "I don't know if you hadn't noticed, but this generator is the source of the temporal rift that's keeping everything here; has it ever occurred to you that, given the perilous nature of reality at this point, what will happen to you if you're here when we deactivate this thing won't exactly be pleasant?"

"That won't be a problem," Marion said, his smile shifting to a glare as he flipped his blade in his hand while glaring at the two TARDIS travellers. "You're never going to-"

His speech was cut off when Amy ran forward, lowering her head to hit Marion between the legs with as much force as she could muster; she didn't trust herself to be able to do much damage by kicking him and it allowed for her to affect a wider area anyway. Despite the throbbing in her head from where she'd hit him, Amy quickly turned around to run after the Doctor as he headed up the walkway, sticking close to the Time Lord to avoid the bursts of green electricity as they quickly reached the top of the walkway.

"OK, so it's a big machine with... some levers; what do we do now?" Amy asked, as she looked at the control console before them with some frustration; after everything she'd heard about this being an attempt to create an invisible ship, she'd expected something a bit more complicated than a massive grey wall with three large red levers on it.

"Pull them down!" the Doctor said, running towards the first lever, Amy following his cue as she ran to the one on the opposite end; it was a little hard for her to reach it, but once she'd stretched up slightly it was straightforward enough to pull it down.

"NO!" Marion's voice yelled from behind Amy as the Doctor grabbed and pulled the middle lever. Amy had just turned around to look at the Faction agent as he charged towards them, his bone-like weapon raised to attack them, before something seemed to suddenly grab him around the waist and yank him back towards the wall.

"The rift is closing, Cousin Marion," the Doctor said, looking scathingly at the Faction agent who'd just been trying to attack them. "And we all know what happens then, I assume?"

"You _can't_-!" Marion began, before he suddenly seemed to collapse in on himself, leaving a brief glow of white light before he vanished into nothing(She briefly thought she saw the Zaralok swimming in reverse, but dismissed it as irrelevant; from what the Doctor had said, it was probably just being pulled back to that portal).

"Done," the Doctor said, looking at her with a smile. "We've sealed the rift, and everything should be getting back to normal."

"But... if the generator being turned off stopped the rift, why's the _Eldridge _still here?" Amy asked, indicating the ship in confusion. "I mean, if the Zaralok and Marion vanished...?"

"Good question, Amelia Pond," the Doctor said, smiling in approval at her before he assumed his 'teacher face'. "To answer it, the _Eldridge _was just sustaining the rift that drew those aforementioned creatures in; the rift that drew it here had been created and closed already."

"Oh," Amy said, nodding in understanding. "Well... that makes sense."

"Right," the Doctor said, smiling at her. "Just give me a few moments to fully muck up the works here, and then it's back to the TARDIS."

* * *

><p>A few minutes later, the Doctor and Amy were standing in the TARDIS, floating in the ocean mid-way between the <em>Eldridge<em>- now a mere historical site rather than the source of a potential temporal rift after the Doctor had removed a few key parts from the generator- and _Poseidon Eight_, watching in satisfaction as pods departed from the fully-illuminated base.

"Ha!" the Doctor said, smiling as he watched the life-pods depart from Poseidon, smiling in satisfaction. "There they go; back to the surface! I dare say daylight never looked so good!"

"What about Dana?" Amy asked.

"Hold on," the Doctor said, activating the TARDIS's radio. "Hello, Poseidon Eight? This is the Doctor and Amy; are you there?"

"_Doctor_?" Dana's voice replied, clearly surprised to hear from him. "_Where are you? You just... and then that_ thing..."

"Cousin Marion is... no longer a problem," the Doctor said, looking regretfully at the radio. "I'm sorry we couldn't save Oswald, Dana; Marion took his place before we even arrived here."

"_It's... it's all right, Doctor_," Dana said, sounding upset even as she reassured him. "_Your meds are helping those who were suffering from the sickness already, but the pods' SOS beacons will bring a hospital ship; we need to get everybody checked out_."

"Good call," the Doctor said, smiling in approval. "Amy and I have already cleared ourselves in our ship, so we'll just be off; pleasure working with you, Dana."

Terminating the connection, he turned to look at Amy with a smile. "We did good today, Pond."

"Yeah..." Amy said, smiling as she looked at the underwater city she and the Doctor had visited.

That whole place only still existed- everyone left in it was only still _alive_- because of her and the Doctor...

She'd probably have a few nightmares about Cousin Marion, of course- they'd actually confronted a _Faction agent_!-, but they'd defeated him in the end, and that was the important thing in this kind of situation.

She'd faced her first challenge as the Doctor's companion, and Amy liked to think that she'd done well; she'd recovered vital ingredients, defeated two minor enemies, and bought the Doctor time when faced with a demented psychopath who belonged to the most terrifying and mysterious group in existence.

She knew why the Doctor wanted her to continue to go to school, but it would just seem so... _tame _after this.

* * *

><p>AN 2: Hope that rewrite of 'Shadows of the Vashta Nerada' met with your satisfaction; a calmer interlude next chapter.<p> 


	16. Musings on Life and Death

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: A short chapter, but I'm hoping for a longer one up next

The History of Paradox

Sitting at her desk going over her history homework- the Doctor had claimed that he had something to work on back at his house, and Aunt Sharon was home this week anyway-, Amy was amazed at how difficult it was to stick to the facts these days.

She'd always found history interesting in the past- although she had these vague memories of sometimes feeling frustrated in class, as though something had said something she couldn't quite believe-, but now that the Doctor was there to give her new insight into everything she was looking at, it was really far more interesting.

Admittedly, she had to be careful what she put down at times- she couldn't exactly say that the Battle of Hastings had nearly turned out a victory for King Harold because a time-travelling alien had tried to destroy the Viking fleet before Harold could fight them-, but that still left her with some broad insight into a variety of topics that she could write about.

Not only was she able to get some interesting insight into what made some historical characters tick- she had particularly enjoyed the Doctor's story about his encounters with Napoleon Bonaparte, even if she couldn't exactly tell her teacher that Napoleon's final defeat was because he allowed himself to lose to stop Earth being conquered by the Daleks-, but she was even able to gain some very interesting bits of information about some more obscure parts about history when it came to writing her report. Her teacher had already praised her decision to write about Winston Churchill's escape from prison during the Boer War as an original concept by focusing on a more obscure part of his history- she'd had to gloss over some of the fine details about _how _he'd escaped without talking about the time-travelling alien conspiracy to manipulate human history for their own amusement-, but she still wished that she could write about some of the _really _unique 'truths' about history that the Doctor had confided in her about.

Still, Amy supposed that was the price you paid for being friends with a time-traveller; you could learn so many secrets of the world around them, but you couldn't share them with anyone if you didn't want to be thought of as insane. It might be amazing to learn that Hitler's secret son had been in charge of a Fourth Reich before it had been discovered and dismantled in 2001, or that Jack the Ripper had been an alien using his murders to control some dark force- the Doctor's manner when discussing those stories suggested that he'd left out some personal details, but what he'd told her was still interesting on its own-, but she couldn't expect anyone else in the world to believe her...

Amy sighed, shaking her head in frustration as she pushed her work away.

Thinking about her homework or thinking about historical secrets wasn't helping her right now; she had to face up to what was really bothering her.

Even if she had no doubt that he deserved it, the fact that she and the Doctor had technically killed someone during their last trip wasn't something that she could just forget, no matter how much she tried to do so.

He might have been a Faction agent, and the Doctor's stories about the Faction had placed emphasis on the fact that 'recruitment' to the Faction typically involved the Faction member killing their own past selves and family to cut themselves out of time meant that he probably hadn't actually existed in _that _sense, but Amy just couldn't quite get her head around it; time travel might be brilliant as a concept, but thinking about that part of it _really _made her head hurt...

Besides, even if he didn't 'exist', it didn't change the fact that she'd witnessed a sentient life stop; that was something that she just...

She hadn't been there when her parents... were taken from her..., but she'd still managed to process the idea of them being gone in the end, mainly because it had just been bad luck and a bad accident; it wasn't as easy to process the idea of someone dying because of _her_, even if he'd been trying to kill her and the Doctor at the time.

The Doctor had assured her that her guilt was a good thing- he wouldn't want to travel with someone who just ignored the consequences of what they sometimes had to do-, but even if she understood his point, it was still hard to accept the idea that she had contributed to ending someone's life, no matter how twisted they were.

As if his death hadn't given her enough to think about, that reference that Cousin Marion had made to her being one of the 'Lost Ones' didn't exactly help her feel much better; the Doctor had mentioned that he was going to try and look into the meaning of that term, but so far he hadn't turned up anything useful, and he was naturally reluctant to try and find rumoured Faction strongholds to find additional information from the source.

Amy would like to believe that Marion had just been trying to freak her out, but something about that phrase...

"Amy," Aunt Sharon's voice suddenly called up to her from the ground floor. "Rory's here."

_Rory_? Amy thought to herself, the dark thoughts of earlier forgotten at this new visitor; no matter what kind of mood she'd been in during his past visits, spending time with Rory's helpful personality and genuinely good nature _always _made her feel cheerier.

Pushing her work to the side, Amy hurried downstairs to where her friend was standing in the door- she could hear Aunt Sharon in the kitchen, but she was probably just getting herself something to eat; she knew that Amy could handle her own meals, so they tended to eat separately given their schedules-, looking at her with a disturbingly neutral expression on his face for someone who was usually so expressive (It was one of the reasons Amy had always liked him; Rory always made it clear what he was thinking most of the time, and he'd never considered her _insane_ for talking about her old raggedy friend even if he'd found it odd).

"Hi, Rory," she said, smiling gratefully at him to try and dispel her more immediate doubts; it had been a while since they'd spent much time together outside of school- particularly when they were mostly in separate classes these days; Rory's courses these days focused on sciences while Amy's were in Drama, History and English-, but she was still glad to see him again. "What's up?"

"You forgot?" her friend asked as he looked at her, the slight hint of hope in his expression fading disturbingly quickly.

"Forgot?" Amy repeated, suddenly uncomfortable as she looked back at Rory. "Forgot what?"

"We were going to the cinema tonight," Rory said, looking at her with a slightly hurt expression. "Don't you remember?"

"Oh... it's Thursday already?" Amy asked, looking up at a calendar on a nearby wall and checking the date on her watch; she'd been so caught up with other things that she'd forgotten that she and Rory had been planning to go to the cinema tonight, given the relatively light homework load from today's scheduled classes. "Sorry, lost track of time..."

"It's... it's fine," Rory said, smiling reassuringly at her as he indicated the car outside the house, accepting her explanation with the same ease that had always made him such a good friend. "Dad's ready to take us off anyway, and we've still got time; you just... weren't answering your phone."

"It ran down and I forgot to charge it back up," Amy said, smiling apologetically at her friend as she cursed her own stupidity; she'd grown so used to the Doctor just turning up when he wanted to see her that she'd forgotten that other people would expect her to rely on her phone. "Sorry about that; I lost track of what was happening."

"Fair enough," Rory said, smiling in understanding before he indicated the car once again. "So... you coming?"

"Just let me grab my coat, and I'll be right there," Amy said, smiling back at him before she turned and hurried back up to her room, grabbing her coat and closing her books on each other so that she could find her place later before hurrying back downstairs to join her friend.

Going to a movie might seem like a strange form of release, but Amy felt that she could use it right now; the chance to watch other people have to make life-or-death decisions on a large scale without having to personally worry about the consequences if _she _made the wrong decisions (She might have only played a minor role in the last crisis, but she or the Doctor could still have died if she'd done something wrong)...

'Relaxing' probably wasn't the exact word to use to describe how she felt about the upcoming trip, but it was the best one that she could think of to use in this situation right now, so she'd go with it until something else came to mind.

It was moments like this, when she had the chance to experience and enjoy the normal life that the Doctor had always told her he admired humanity for being able to live- a world where trips to the cinema to watch people live out incredible lives were the highlight of some peoples' weeks-, that made her almost regret what she had planned; she was really going to miss Rory Williams when she finally left Leadworth to travel with the Doctor...

But she had to.

She just _couldn't_ stay here on Earth after everything that the Doctor had told her about the universe beyond her planet; even the thought of travelling to other countries seemed small compared to the possibility of going to other times and planets in the TARDIS.

Rory would miss her when she left, but it wasn't enough for her to want to remain on Earth when she could go virtually everywhere else in time and space.

Besides, Rory spent too much time with her as it was; maybe once she was gone he'd finally manage to find a decent boyfriend...

* * *

><p>AN 2: Just to remind the readers, in the flashbacks of 'Let's Kill Hitler' Amy mentioned that she'd always assumed that Rory was gay before Mels revealed how he felt about her; without Mels in this reality, Amy naturally has no reason to assume that Rory's straight based on available evidence.<p> 


	17. Caught in the Web

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Another jump forward, this time to approximately Christmas of the same year; a shorter chapter, but I felt that it explored a few personal developments that the Doctor needed to explore, and I do have a particular rewrite coming up that you won't be expecting...

The History of Paradox

"Ah," the Doctor said, smiling as he stepped out of the TARDIS, taking in the world before them with a satisfied smile before he turned to look at his companion. "Amelia Pond, I give you Metebelis Three!"

As she walked out of the TARDIS, curious to see the location where the Doctor had taken her for an early Christmas present- he was working on something for her in the TARDIS, but all he would say so far is that he hadn't finished it yet-, her eyes widened as she took in the incredible view awaiting her. The TARDIS was standing on a wide ledge, mountains rising behind it and a beautifully blue lake spread out before them, surrounded by a green forest that extended out from the other mountains, a blue moon shining down on the planet to create an even more incredible atmosphere as they took in the world before them.

"Just for a visit, of course; it might be Christmas, but I don't have the authority to give you a planet," the Doctor added, smiling warmly at her before Amy turned and enthusiastically hugged him around the waist.

"Thank you thank you thank you!" she said, grinning as she pulled away from him to take in the view around them once again. "This is... I mean..."

"Yes, I know what you mean; beautiful area, isn't it?" the Doctor said, smiling at her approval. "My history with this place has had its ups and downs- a couple of close calls due to some natural flukes-, but it's past the worst of its era; most of the problems are out of the way now."

"Problems?" Amy asked, looking curiously at him.

"Not important right now; like I said, they're past the worst of it by this point in history," the Doctor said, shrugging dismissively as they began to walk down the mountain. "Come along, Pond; time to show you what this place has to offer."

After their encounter with Cousin Marion, the Doctor's lessons had shifted their focus from warning Amy about the potential dangers she could face to talking about some of the natural and manufactured sights they could witness in their travels; with Amy having proven herself under fire, the Doctor felt justified in giving her a chance to appreciate the better parts of travelling with him, in order to ensure that she didn't feel too scared at the prospect. He'd thought about taking her to check out one of the wonders of the universe, but after his close call with the city of the Exxilons, he felt that a visit to a calmer location of natural wonder would be for the best.

Besides, as he followed Amy down the mountain and through the deeper forests of the planet, able to relax as he pointed out some of the scenes of natural wonder around them, ranging from the tall trees to a few of the more peaceful examples of local wildlife- evidently conditions were improving now that the spiders were no longer active to cause problems; the last time he was here all he'd seen apart from a spider was a roc, and those birds were so large it would have taken a miracle for the spiders to have any kind of impact on them-, he had to admit that he was still rather fond of this planet.

True, he'd all but died here in his third incarnation- the Faction might have managed to 'jump ship' and preserve the timeline where he'd died on Dust for _them_, but as far as he and the rest of the universe were concerned his third self had died of radiation poisoning while fighting the giant spiders and that was that-, but he couldn't allow that to affect his memories of the planet's natural beauty and incredible wildlife (When you were able to avoid the rocs, anyway)-

The sound of something hissing cut off that particular train of thought, but the Doctor still barely had time to turn around before he found himself pinned to the ground with something biting him in the neck, Amy's screams of fear the last thing that reached his ears before he lost consciousness...

* * *

><p>As he blinked his eyes open once again, the Doctor cursed to find himself tied up in yet another giant web; getting stuck in this thing once was just acceptable when he didn't know what to expect, and the second time was also excusable given that he'd been in a bit of a funk at the time, but being trapped three times was just ridiculous.<p>

Looking around, he was relieved to see that Amy was just next to him, evidently alive but still unconscious and there was no sign of the spider that had attacked them; evidently, like its smaller cousins, it preferred to give its prey some time in the web before it decided to feast itself. They were currently in the mouth of a small cave, just far enough inside it to prevent them being seen by the rocs or other large predators, with the forest they'd been walking through visible outside it;

Refusing to give himself the chance to panic, the Doctor set to work on working his way out of his current bonds, giving himself a few moments to recall some of the old tricks he'd picked up from Harry Houdini- he wasn't exactly in his most physically capable body right now, but he wasn't exactly a slouch either- before he started to work away at the webbing keeping him contained, his fingers seeking out a few gaps in the webbing around him (Luckily he hadn't had time to cut his fingernails recently; he could generally moderate their length as he saw fit, but when living among humans long-term he thought it only polite to try and present as normal an appearance as possible, which included letting his nails grow). In a few minutes, he'd managed to find some appropriate gaps and enlarge the area around them accordingly, giving himself a few more moments to work at his spider-made bonds before one had finally emerged, just as Amy was beginning to stir.

"Ow..." she said, her voice worryingly weak as she looked at her surroundings for a moment, before her gaze focused on her friend. "Doctor, what's-?"

"We've been captured by one of the last of the giant spiders of Metebelis Three, and I'm sorry I didn't mention them earlier, but I honestly thought that they were extinct," the Doctor said, looking apologetically at his young companion as he felt around behind himself before his hand finally settled on a rock of the appropriate shape for his current purposes; a decent size and with one edge notably sharper than the others, it would make a convenient 'knife' for the current purposes (Apparently the spiders were becoming more careless; the 'Eight-Legs' would never have left him somewhere with this many convenient potential weapons, no matter how secure they might believe their webbing to be).

"G... giant spiders?" Amy asked, a slight tremor in her voice as she looked at the Doctor. "H... how did that happen?"

"Oh, they were on board an Earth expeditionary ship that crashed here a few decades back, with the unique radiation of Metebelis Three's blue crystals creating a mutative effect that allowed the spiders to achieve sentience and some degree of psychic powers," the Doctor explained, smiling briefly at Amy to try and reassure her- she might be braver than most girls her age even before he met her, but she was still entitled to be scared in situations like this- while he continued to work at his bonds. "I defeated their first attempt to create a psychic network to facilitate galactic conquest by overloading the crystal lattice they'd been putting together- too much power really can be a bad thing, you know-, but a few of them managed to escape the worst of the feedback; I thought most of them had been wiped out, but it looks like a few are still hanging around somewhere."

"Their... _first _attempt?" Amy asked, looking apprehensively at the Doctor, the rest of his words of reassurance apparently forgotten in the face of that particular newsflash. "As in, they attempted more?"

"Just one more to my knowledge- they'll attempt an invasion of Earth a few years from our home time-, but you don't need to worry about that; I stopped it a couple of centuries ago," the Doctor said with a smile, waving his now-freed hand at her as he finally managed to cut through a few significant strands in the network of webbing binding him in place.

"You mean... you stopped it when you were a couple of centuries younger... a few years in my future?" Amy asked, looking slightly uncertainly at the Doctor; she was generally good at following the shifting tenses and terms used when dealing with time travel, but clarification was always helpful.

"Exactly," the Doctor said, nodding at Amy with an approving smile; describing the tenses of time travel in English was always tricky, but Amy seemed to be getting the hang of it well enough. "I'm pretty sure the aftermath of that defeat left them incapable of trying something like that again- nothing like being caught in the psychic backlash of the planet you just conquered forgetting about you to discourage you trying that kind of thing again, after all-, but that doesn't mean that a few of them weren't still hanging around here; I suppose I'd been overly optimistic about how poor their chances of survival actually were."

He sighed slightly as he refocused his attention on the webbing for a few moments, smiling in relief as he finally got another hand free. "I mean, you'd think that suffering the consequences of two major psychic feedbacks would be enough to convince a species to abandon the idea of pursuing sentience that was only created by a radioactive accident!"

"Uh..." Amy said, stuck for anything that she could usefully say in response to that statement, even as she smiled to see the Doctor working his way free of his previous prison.

"Never mind; that's not important right now," the Doctor said, one arm now free as he continued to cut away at his bonds. "What's important is that one spider isn't a serious threat now that we know it's there; if I can just find the right tools..."

"Uh... why are you taking so long to get out?" Amy said, glaring briefly at him, desperately seeking anything that would take her mind off the fact that she was potentially about to be eaten. "I thought you met Houdini?"

"Yes, but it's been a long while since then, and I'm not exactly built for that kind of manoeuvring these days; I was a lot more... _flexible_ a couple of centuries ago..." the Doctor said, wincing as he accidentally jabbed himself in the arm with his rock-blade before he continued to work at freeing his other side. "Besides, Houdini could get out of everything, but it wasn't as simple as some of the stories sound; it's all a matter of patience- _Geronimo_!" he said suddenly, grinning as he freed his other arm from confinement and began to work his legs free of the webbing that still kept them immobilised.

"Are you sure that's safe?" Amy asked, looking anxiously at the Doctor. "What if the spider comes back... or what if more show up?"

"Unlikely, really; any large groups of spiders together when I created the feedback circuit would have been fried from the psychic force of the network breaking down- too much mental energy in one place, you know-, and I doubt they'd be smart enough to realise that it was a one-off occurrence in the absence of the Great One," the Doctor explained, quickly severing the webbing around his legs before he stood up, stretching his stiff limbs before he walked over to Amy and began to cut at the webbing keeping her confined. With both arms fully mobile and able to get a better angle for his attack, he was soon able to cut through the webs holding his friend's arms, before quickly moving on to cut away at her legs.

"Doctor..." Amy said, her voice suddenly apprehensive.

"Nothing to worry about, Pond; we've just got-" the Doctor began, before he heard a scuttering sound that he would never forget. Spinning around, he found himself staring at a large spider approaching them, its mandibles bared and a hungry expression in its eyes as it prepared to leap towards its two former victims; with Amy's legs still trapped, all it would need to do would be to paralyse the Doctor and then it could re-bind them.

"NO!" the Doctor yelled, charging at the spider and intercepting it mid-leap, leaving it practically hovering him as he fell to the ground, his right arm keeping the spider away from his face as its mandibles clicked maliciously just in front of his eyes. The Doctor desperately scrabbled around in the nearby dirt as he tried to find something that he could use to hit his opponent, but he was currently outside the cave, with the largest thing near him being a branch that he'd never be able to take hold of in time to hit this thing with enough force-

His thought was cut off as something large and heavy struck the spider in the side, knocking it away from him, followed by another object a few moments later as he was still regaining his wits that struck the spider with an audible thump.

Sitting up after a few moments had passed with nothing but silence from the spider, the Doctor had to smile in approval at the result; a large rock had struck it in the side, apparently damaging some of its legs judging by the way they were bent, and a larger rock had landed on top of it, completely covering its upper body and leaving only a few twitches from its legs to show that it had ever been alive.

"A rock for a spider, mmm?" the Doctor said, looking at Amy with a smile of approval as his companion stood beside him, her arms still outstretched in the position she'd assumed to throw the rock at the creature attacking him, the last strands of webbing that had been holding her immobile lying draped on the ground around her; she must have cut the webs around her legs while he was keeping the spider distracted.

"I didn't have a big enough shoe," Amy replied, grinning back at him with a casual manner that almost disturbed him before he recognised the edge of apprehension in her eyes; she recognised the scale of what she'd done, but was simply putting it aside until she was more prepared to face it.

"Well," the Doctor said, grimly studying the large rock that was the only sign that a creature had been there. "Good toss, Pond."

"Thanks," Amy said, smiling back at him even as she still visibly trembled, reminding the Time Lord of the most important thing to attend to right now.

"I'm sorry about that," the Doctor said, moving over to place a comforting, apologetic hand on the young girl's shoulder, indicating the spider's body. "You shouldn't have had to deal with something like that-"

"I wasn't scared," Amy suddenly interjected, looking back at the Doctor.

"Because I was there-?" the Doctor began to ask, suddenly wondering if he was helping or restricting Amy with his lessons.

"Because I know you'd do _everything _you could to keep me safe," Amy replied, smiling back at him for a moment, as though wanting to ensure that he understood her meaning, before her smile faltered. "You don't need to be there, Doctor; you just... I just..."

"I would _never _abandon you, Amelia Pond," the Doctor said, kneeling down slightly to look her more directly in the eye- she was still growing, but she wasn't quite done yet; she was still at least a head or so shorter than him- as he registered what she was trying to say.

She might have faith in him, but there was always going to be that small part of her that remembered how he'd left her over eight years ago and didn't get back until last year...

Still, even if that part remained, the Doctor would do everything he could to keep it quiet; he had left Amelia Pond behind once, but the more time he spent with her, the more that he was grateful that he hadn't done it again.

After so long travelling alone, on the run from his greatest enemies, thwarting their plans where he could and trying to preserve the legacy of his people where possible, it was almost refreshing to have someone show such faith in him...

"Come on," he said, taking her hand with a smile, "let's have another look around before we head back, shall we?"

Grinning at this offer, Amy tightened her grip on the Doctor's hand for a moment before they began to run through the woods around them once again, their initial fear forgotten when faced with the joy of the world they were now visiting.

As far as Amy was concerned, life with the Doctor might be dangerous, but with him to protect her and the skills that he was teaching her, she had faith that she would always be safe, no matter what opposed them...

* * *

><p>AN 2: Short, but I like it; coming up, another episode rewrite, featuring the Doctor meeting some VERY particular people once more...<p> 


	18. Marooned in the Wastelands

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: As promised, a new take on a very particular story, as Amy meets some former companions for the first time...

We don't get into the action of that story yet, but it should be obvious what's coming up, so I hope you like my 'prequel' before we get to canon.

The History of Paradox

"This is it?" Amy asked, looking out at the large wasteland spread out before the TARDIS's entrance, two moons just visible in the sky and a red tint seemingly surrounding the entire planet, along with large piles of wreckage scattered around them.

When she'd dropped in on the Doctor to inform him that school was closed due to a nasty bout of food poisoning among the staff, she'd naturally been expecting the subsequent offer of a trip, but she hadn't been expecting it to be somewhere so... lifeless.

"The wasteland of the Crimson Heart," the Doctor said, smiling in satisfaction at the sight in front of him before he looked back at Amy with a slight shrug. "Probably wouldn't have come here now, but I picked up a signal from this area, and, well, why not take a look? We need something simple after what happened last time, and this is perfect; an excellent excuse to have a wander around a quiet, deserted planet with nothing to worry about but some old bits of wreckage that I know neither of us will examine too closely if it might be dangerous."

"Uh... in other words, we're basically acting like archaeologists?" Amy asked, looking uncertainly at the Doctor.

"Well, it's a fresher environment than what most archaeologists would work with, but... you're basically right, yep," the Doctor said, looking back at Amy in time to notice the slightly teasing smile on her face. "Why?"

"What happened to 'I point and laugh at archaeologists'?" Amy asked, smiling as she recalled a story that the Doctor had once told her; that incident with the Library might have been scary, but there had been something amusing about it, even if the Doctor hadn't explained exactly how it had been resolved...

"We can't progress if we can't look at the past, Pond, and considering the mysteries surrounding this battlefield I'd like to know more about what we're up against before I start looking into its past," the Doctor explained, shrugging slightly as he looked back at her. "Besides, this isn't archaeology; that involves digging and the acquisition of expensive equipment to see something broken that I can look at when it's intact, but this is just having a poke around to see if we can anything interesting."

"So... this is a treasure hunt rather than archaeology?" Amy asked.

"Precisely; archaeology is based on finding clues for anything, but treasure hunts are based on finding something _very _specific and _very _interesting," the Doctor said, grinning at her as he indicated the nearest debris. "Shall we?"

"Why not?" Amy replied, smiling at the Doctor in understanding as the two of them walked over to the nearest pile of rubbish and began to search through it.

It might not be in the thick of the action, but after everything that she and the Doctor had been through on their last trips, Amy had to admit that this trip looked like it would be a different but interesting- and, more importantly for the moment, less potentially dangerous- kind of trip.

* * *

><p>As the two of them spent the day moving through the piles of wreckage, Amy had to admit that the Doctor had been right; this was actually a surprising amount of fun. Not only did the Doctor enjoy telling her about the battle that had left the planet in its current condition- apparently there had been-, but he was even able to provide her with some descriptions of the ships that the parts they were studying were likely to have come from, based on factors such as the manufacturers of the device they'd found or the metallurgical content of the hull, as well as the history of the area and the races they'd been in contact with before the war.<p>

It might just be another form of school, but the difference between this and schoolwork was that the Doctor actually brought it to life on a constant basis; it was the ultimate field trip with no limitations on what the lessons would be about.

"So... after all that effort, they just destroyed themselves?" she asked, looking sadly at the Doctor as he finished telling her the story of the battle.

"Last gambit of the last few ships in the fleet according to all reports," the Doctor said, his expression grim as he reflected on the stories he'd heard. "The ships on one side had virtually drained their weapons, and the opposing ships had sustained serious engine damage; the only thing the first side could attempt was a last desperate charge, one side setting a collision course while the other side fired everything, and they each pretty much tore each other apart in the process."

"That's..." Amy began, before she trailed off, uncertain about the merits of continuing that sentence without coming across as insensitive.

"Stupid?" the Doctor finished for her, reassuring Amy on that front; if the Doctor had expressed a positive opinion of the fight, Amy could have known that it was over something worthwhile, but the fact that he hadn't said something positive suggested to her that there was nothing positive for him to say.

"Exactly," Amy said, smiling in relief.

"Well, it was," the Doctor confirmed. "They were basically just fighting to control a planet that was in a strategically important situation in their formerly cold war- beat the other side to it before they gained enough of an edge; think of it as the interstellar equivalent of Cuba, you know-, and then, when their fleets tore each other apart, they decided to back off and leave the planet on its own..."

His voice trailed off as he looked up, something attracting his attention away from the pile of wreckage that he was studying that Amy couldn't see. "Hold on... hyperspace distortions?"

"Pardon?" Amy asked, looking at him in confusion. "I don't-"

"It's one of my peoples' additional senses- I don't always register it because I prefer to focus on the human level, and it's not something I'd normally be aware of if we weren't in an atmosphere unless I was trying or it was _really _powerful-, but there's something..." the Doctor said, his voice trailing off as he looked around.

"What is it?" Amy asked, her apprehension growing as she looked at her friend; after all the times she'd seen the Doctor looking in control no matter what they encountered, just the idea of him looking confused about this situation was enough to worry her. "What's causing that… distortion?"

"I'm not sure..." the Doctor said, his expression thoughtful as he continued to study the field of wreckage surrounding them before pulling out his sonic screwdriver. "There's definitely nothing actually _active _here; I would have detected it when we were arriving..."

Just as the Doctor had spoken, a large ship that put Amy in mind of a large vulture or a Klingon ship from _Star Trek_, with an extended 'neck' and long wings, came down from the sky, emerging from the clouds above them and moving at incredible speed towards an area that Amy was fairly sure she recognised; there was something about that antenna-like thing at the top of one pile...

"TARDIS!" she yelled in realisation before she turned to the Doctor. "It's-"

"Heading for the TARDIS; come along, Pond!" the Doctor said, hurrying towards the location where they'd left their precious blue box, Amy following him as quickly as possible.

Even as they ran, however, both of them knew that it would be too late. They were barely half-way back to the location where the TARDIS had materialised before they saw the ship taking off, a small blue object just visible underneath it, moving up to the main ship, apparently drawn to the other object by what Amy was automatically inclined to think of as a tractor beam…

"The Claw Shansheeth of the Fifteenth Funeral Fleet?" the Doctor said, looking at the ship in confusion as it vanished into the dark atmosphere above them.

"Who?" Amy asked.

"They're basically the funeral directors for fallen galactic heroes; they come after major battles and take fallen heroes back to their homeworlds," the Doctor said, briefly automatically slipping into his 'teacher mode' before he returned his attention to the more obvious question facing them, his gaze focused on the departing ship. "But that doesn't make sense; why would they come here, and why would they steal the TARDIS?"

"Well... maybe they got tired of it?" Amy asked, seizing on the most obvious answer to her friend's question.

"Tired of it?" the Doctor repeated, looking at Amy in confusion. "Tired of what?"

"Of always _seeing _all that death and not being able to do anything about it?" Amy asked, recalling some of the tales she'd heard in history about people becoming disillusioned with war after finding out more about the people they'd killed on the other side. "I mean, if they just keep seeing people when they're dead- particularly if it's a conflict like this; you said yourself that nobody really _won _anything after the fighting here was over-, maybe they..."

"Decided to take my time machine and use it to stop all that death?" the Doctor finished for her, nodding at her with a slight smile. "Good thinking, Pond; took what you knew about the situation at hand, applied it to present a practical theory, and clearly explained it."

He looked thoughtfully up at the sky in the direction that the ship had departed, a thoughtful expression on his face. "Of course, even if we assume they were responsible for the signal that drew me here, that doesn't explain why they just left; I locked the old girl before we left and the key's still in my pocket, and while the Shansheeth aren't exactly stupid, they definitely don't have the technology to make themselves a substitute key without... without..."

His voice trailed off for a moment as he continued to stare up at the sky, his eyes widening in realisation before he looked sharply back at Amy. "What's the date right now?"

"What-?" Amy asked, before the Doctor reached into his pocket and pulled out various objects, finally removing what looked like a large old-fashioned watch, which he held up in front of his face and waved around for a few moments before he smiled in understanding.

"Just under a year since I saw him; close enough," he said, smiling as he looked at Amy.

"Saw who?" Amy asked, looking at the Doctor in confusion, even as he turned and ran towards the nearest pile of junk, quickly starting to rummage through it with a speed that was faster than she'd ever seen him move. "Who are you talking about... and what are you doing?"

"Working on something that will take me to Earth," the Doctor said, pulling out a few parts as he began to use the sonic on them.

"And... that's going to help us?" Amy asked, looking in confusion at the Doctor; he might have been giving her some pointers on how to steer the TARDIS and some of the basic examples of technology they might encounter, but what certain bits of advanced technology were meant to do still confused her, and right now she couldn't see what the Doctor was trying to assemble. "But how can you know-?"

"Because," the Doctor said, looking back at her with a smile, "as intelligent as the Shansheeth are, they _aren't _intelligent enough to work out how to open the TARDIS with anything they've got on their own, but they _may _have some technology that could recreate it if they have access to the right resources, and those resources include certain things that they can only find in this time period if they keep going in their current direction on Earth..."

"Oh," Amy said, stuck for anything else to say as she looked at her friend. "So... what are you doing?"

"Well," the Doctor continued, picking a few more parts out of the junkyard as he continued to speak, "a few months before we met- actually, it's been about that long from their perspectives according to the calendar-, I was visiting a friend to protect her from the Trickster- pan-dimensional being who serves as a manifestation of the Pantheon of Dischord, and that's another long story that I'll tell you later-, and one of _her _friends became charged with the artron energy of the TARDIS when he and the old girl were stuck in a temporal trap."

"Oh," Amy said, stuck for anything else to say.

She thought she recognised some of the terms that the Doctor was using, but that didn't mean that the sentence itself made sense; what exactly was a 'temporal trap' in this context anyway?

"So... how does that help us now?" she asked, deciding to focus on what was most relevant; she could ask about the other things later.

"On its own, it wouldn't; it'd just be another interesting story," the Doctor said, before he pulled a small gold object with a green gem in it out of his pocket. "But with _this_ taken into account, it's another matter altogether."

"What's that?" Amy asked.

"A spare artron energy cell," the Doctor explained with a grin, as he began to work at a small rod for a few moments before attaching the energy cell to the end of it. "Considering how I lost the old girl before... well, things happened; let's leave it at that... I decided that it would be a good idea to keep this kind of thing around; in the event of me falling into a parallel world where the TARDIS loses its link to the remnants of the Eye of Harmony in this world- the Eye was originally stretching out across all known dimensions, but with Gallifrey's destruction its influence is limited to this plane of existence, and I need to occasionally recharge her to retain that much-, this power cell provides me with a short amount of reserve power that I can use to return to my home universe."

"But what good does that- _oh_," Amy said, her eyes widening in understanding. "If it's from the TARDIS..."

"_Exactly_," the Doctor said, grinning proudly at her. "With this energy cell to provide me with a sample of the TARDIS's natural artron energy- and assuming that I can find the relevant parts around here-, I should be able to set up the necessary equipment to initiate a very complicated biological swap across ten thousand light-years by using that friend as a receiver, allowing me to travel to Earth by focusing on the artron energy within him as a beacon, track down the Shansheeth, recover the TARDIS, and return for you in a matter of moments, and _that _is the _worst _case scenario."

"Oh," Amy said, smiling hopefully at him. "That's... good, right?"

"Well, it would be good, if it weren't for the fact that I can't be certain why the Shansheeth would take the TARDIS to Earth and therefore can't know how long it would take me to find the old girl," the Doctor explained. "They should be able to get there in a day or two- their ships have to be fast, after all-, so I should have it ready in time, but whether they'll be in a situation that will make it easy for me to find her when I get to Earth is another matter."

Amy was briefly anxious at the reference to them potentially being here for a couple of days- they didn't have a thing to eat and she hadn't seen anything to eat on this planet; how would they survive?-, but she forced that issue aside and tried to focus on the fact that they had a way to get out of this mess; she could manage without food for a couple of days, right?

"But… you can get us home, right?" she asked, looking at the Doctor as he continued his work. "Once you've finished this?"

"Well… yes and no," the Doctor said, looking apologetically at her.

"Yes and no?" Amy repeated.

"Even if I'm right and we make it back to Earth, we'll be a few years in the future from your perspective, so our priority will be getting back to the TARDIS rather than going back to Leadworth- the moment we _learn _if we did or didn't get back we run the risk of creating a paradox-, and even then this isn't exactly top-of-theline equipment we're working with here," the Doctor said, sighing as he paused in his work for a moment and studied the sonic screwdriver. "From what I've seen of the material available to me, I'll need the sonic's power source if I'm going to make this mess actually work- the artron cell will be needed to set up the biological swap-, which means that I won't be able to get it as refined as I'd like; unless I can get a substitute at the other end, this is going to be relatively unstable..."

"Unstable?" Amy asked, her mind seizing on the potential negative connotations of that word. "Does that mean-?"

"It just means that I might not be able to set up a permanent transport at the moment; we can worry about that once we know whether we're actually going to be able to leave here in the first place," the Doctor said, before he put his hands into his pockets and pulled out something else that he subsequently tossed over to Amy. "Oh, and while we're waiting, you might like these."

Looking at the object that the Doctor had just passed to her, Amy was slightly surprised to find herself looking at nothing more than a couple of ham sandwiches in a plastic container; it looked like the Doctor had brought them from the local convenience store in Leadworth.

"Uh... thanks," she said, looking back at him, slightly taken aback at his anticipation of her food-related concerns before she'd even voiced them. "Do you-?"

"Had a good snack before we left; I'll be fine," the Doctor said, smiling reassuringly at his friend. "Just focus on keeping yourself together and fed, and I'll do the rest; we'll be back before you know it."

Amy knew that she should feel more optimistic at the news that the Doctor had a plan, but it was hard to focus on something like that when faced with a barren alien planet after your only means of departure had been taken from you.

She'd faced danger with the Doctor before, but back then the TARDIS had always been there as a way off; this time they didn't even have that as an option...

All they had was a plan that even the Doctor admitted might not work, relying heavily on several assumptions that were based on theories that felt more like guesses than anything Amy had heard from the Doctor before now.

She might believe in him, but when her dear madman with a box had lost his box… was anything possible?

* * *

><p>AN 2: I take it you can guess which story is coming up next?<p> 


	19. Initiate Artron Biological Transference

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Hope this meets with your approval; writing the other side of the transference was _not _easy…

AN 2: For those who don't know, the Doctor's reference to an encounter with the Tractites refers to the Eight Doctor's meeting with Jo Grant in the novel 'Genocide', when a group of Tractites- horse-like aliens whose planet was conquered by Earth's empire at some future date- went back in time and changed history to erase humanity from existence; Jo was unintentionally dragged back in time along with the Tractites' human ally when a friend asked her to investigate what turned out to be their time machine.

Considering that most of what was revealed about Jo's life in the novel was contradicted by later events- she only had one son and was divorced from Cliff while working two jobs-, I'm assuming that the Doctor was able to 'tweak' things slightly while returning Jo home to give her a better life, exploiting the fact that history was being rewritten already, thus accounting for her more positive past in 'Death of the Doctor'

The History of Paradox

"Done!" the Doctor said, grinning over at Amy as he inserted the sonic screwdriver's power crystal into the device in front of him, slipping the top component off before putting it all back together again.

"That's it?" Amy asked, looking curiously at the Doctor's latest invention. It was basically a pillar, about a head or so shorter than Amy, with a base of four metal bars around a blue half-globe at the bottom, with silver bars around a copper inner tube extending upwards to a blue column about the height of the Doctor's hand with handles around it, topped off by a thin copper top that was linked to the lower base by a series of wires. The Doctor had placed the artron crystal in the middle of the column before attaching the top, and had already used it and the screwdriver to make a few transmissions to Earth.

"Uh… are you _sure _those… signals… you sent earlier… actually made it?" she asked, unable to conceal her uncertainty from her friend; after so long thinking of the Doctor as the 'madman with a box'- as he'd proudly proclaimed himself to be on one occasion-, she thought that it was only natural to be worried now that he didn't have the box any more.

"You heard the way this thing hummed, Pond; add in to the readings I took on my screwdriver, and I'm certain that everything's under control," the Doctor said, smiling reassuringly at her with the kind of quiet confidence that Amy doubted he could fake; he might gloss over some parts of the truth sometimes to 'protect' her, but Amy had faith that the Doctor would never _lie _to her.

"But… why did it need the screwdriver's battery?" Amy asked, uncertainly indicating the device. "You already used it without the battery…"

"Oh, those uses were just to ensure that everything was working; if I'm going to establish the switch, I need to ensure that this thing has a constant source of power rather than just whatever energy's left in the cell," the Doctor explained with a nonchalant smile. "I've determined that the link I'm going to be using to send myself to Earth still exists, so all I need to do now is establish a temporary telepathic connection to confirm that Clyde's in a suitable environment- I don't exactly want to switch with him when he's at school or something like that, after all-, and all's sorted."

"School?" Amy repeated in surprise; nothing had been mentioned about Clyde still being at school that she could recall.

"Clyde's in his mid-to-late teens- I didn't get the chance to establish specifically which it was when we last met, and it's been a while since I've seen him anyway-, so there's a chance he'll be there; as I said, he mainly works with an old friend of mine rather than hunting aliens himself," the Doctor explained, before he turned his attention back to the machine. "Right now, prolonged transference is the main problem here…"

"Hold on; what was that about a telepathic connection?" Amy asked, going over the more complicated parts of the Doctor's previous sentence in her mind as he turned back to his equipment. "You can… you can read his mind?"

"Well, I was better at it when I was younger, and it's normally touch only; I can only do it in this situation at this distance because Clyde's connected to the TARDIS's artron energy and the TARDIS's energy is similar to mine, so as long as I keep my thought processes focused, it should be enough for me to make contact with him without causing any brain damage before I initiate the swap," the Doctor said, pausing in his work to look directly at Amy as he guessed her main concern. "Amy Pond, whatever else I might be capable of, I will _never _use that ability on you without your permission unless I am certain that there is no other choice."

Despite her initial paranoia and shock at the news- she was having enough trouble processing her thoughts on her _own _without someone else reading them-, Amy only had to look in the Doctor's eyes to believe him.

He had let her down when he had left her so abruptly, but it had been made clear more than once since then that his mistake had been due to nothing more than the damage sustained by the TARDIS when… something bad- he still hadn't told her precisely what, but she hadn't asked either- had happened; he'd _never _do something like that on purpose.

The Doctor waited a moment to ensure that Amy had understood him before he turned his attention back to the device in front of him. Tapping it once or twice with his knuckles, he listened to the sounds it made in response before nodding in satisfaction, placing his hands directly on the upper part of the device for a few moments as Amy watched.

The device had established a connection to the artron energy on Earth in Clyde; now he just needed to get through that and establish the link to Clyde himself…

Reaching out with his telepathic senses as he began to tune out the humming and blinking lights on the device in front of him, he spent a few moments probing around to initiate contact with the artron energy in the cell- complicated, but he'd done enough reading on the manipulation of biodata after that mess with Griffin that mentally interfacing with artron energy was a cinch by comparison- before he reached out along the connection between the energy here and the energy on Earth, his mind swiftly finding what he was looking for…

"_Sarah Jane_," the Doctor 'heard' as his mind began to gradually establish a connection to Clyde- creating a visual connection would be too difficult, but an auditory one should be enough to help him work out where he'd be arriving-, "it's the Shansheeth; they're lying through their beaks! They want you and Jo; this whole thing's a trap!"

"I knew it!" Sarah Jane Smith's voice said, answering the Doctor's immediate question- Clyde and Sarah were in proximity to each other, and they were talking about the Shansheeth at a relatively high volume, which made it at least somewhat likely that they were somewhere relatively private.

"Hold on!" another voice said- a voice that the Doctor only needed a few moments' thought to recognise; Sarah made sense, given Clyde's history, but what was Jo Grant doing with them?-, a familiar sense of hope to her voice that hadn't been there during their last tragic meeting with the Tractites (Hopefully that meant that his slight gambit at taking a detour to talk to Cliff in the past had paid off). "If they're lying… that means the Doctor's still alive!"

"Of course I'm still alive, Jo!" the Doctor said, the psychic link he'd created allowing him to speak through Clyde's mouth even if he couldn't see anything yet. "I would've thought that was obvious; catch up!"

"I beg your pardon?" Jo's voice said again, sounding shocked and indignant at Clyde's apparent rudeness.

"Clyde?" Sarah asked, the maternal concern obvious in her voice. "Is that you?"

"Course it's not, it's me!" the Doctor said, hoping that Clyde was facing in the right direction; hearing wasn't exactly a good means of judging where someone was in this situation. "I'm using Clyde as a receiver; I've keyed into his residual artron energy to organise a very complicated swap across ten thousand light years. Hold on."

With that said, the Doctor found the connection temporarily terminated, leaving him looking at Amy with a suddenly-darkened left hand.

"What-?" Amy asked, looking at him in confusion.

"Just initiated a partial swap between me and Clyde; right now, we've only exchanged a temporary projection based on the perception filter so that his hand looks like mine and vice-versa," the Doctor explained, before he turned his attention back to the device in front of him. "Now then, just let me get everything back on…"

With that brief explanation, he activated the artron surge again, feeling the energy surge around him as he sensed his surroundings change, the telepathic link he'd formed with Clyde allowing him to be peripherally aware of the teen's mind.

"Sorry Clyde!" he said, straining to engage the full artron switch- at this point it was a matter of mental strength rather than the equipment he was using- as he felt himself briefly shift back to the Crimson Heart between words, "but this- space- is- taken!"

With that word, the transference finally completed, and he was standing in a corridor on Earth- most likely a military base of some sort; their corridors were always distinctive due to their essential simplicity-, facing Sarah Jane and Rani Chandra- relatively unchanged since their last encounter at Sarah's wedding- alongside an older Jo Grant and a young man, taller than Jo, with dark hair dressed in a blue turquoise T-shirt, all looking at him in shock.

"So," he said, looking at the group around him with an awkward smile- arriving that way wasn't exactly a conventional way to travel even if he hadn't swapped places with someone in the process-, "gosh, that was different; hello, everyone!"

"Who are you?" Rani asked, the shock shifting to an intense glare that reminded him of the expression assumed by Rani's Time Lord namesake when she was particularly annoyed. "Where's Clyde?"

"Come on, Rani, use your brain!" the Doctor said, looking promptingly at her. "Clyde and I swapped places, right; I'm where he was, he's where I was, which means…"

His voice trailed off as he realised the implications of the current situation; he'd been so focused on getting away from the Crimson Heart that he hadn't stopped to think about how Clyde would cope with things at the other end.

"Oh," he said, his smile faltering. "That _could_ be a problem."

He trusted Amy and Clyde's ability to cope with being stuck on the planet for however long it took to deal with this, but it wasn't exactly fair to ask them to be forced to rely on a relative stranger- particularly in Clyde's case, since he'd at least told Amy who Clyde was- on an unfamiliar planet in the middle of a mess where he was still trying to work out the motives of his enemies in the first place…

* * *

><p>"What the…?" Clyde said, looking at his surroundings in confusion.<p>

One minute he'd been standing in a corridor, and now he was on some barren red planet, surrounded by rubble…

"You're… Clyde, right?" a voice said, prompting him to turn around and look at the sight of a red-haired girl, maybe slightly younger than him, dressed in somewhat subdued clothing of a denim jacket and trousers.

"Uh… and you?" Clyde asked.

"Amy Pond," the girl replied. "I'm with the Doctor."

"The Doctor?" Clyde said, his eyes widening with new hope. "The Doctor's here?"

"He… well, he _was_," Amy said, looking awkwardly at Clyde. "He… you just switched places with him."

"_What_?" Clyde said, looking at his surroundings in renewed frustration.

He finally had the chance to visit an alien planet, and it was something that looked like a Martian junkyard without any way back, and it was _the Doctor's _fault?

Why would he _do _something like this?

* * *

><p>"You bring him back, <em>whoever you are<em>!" Rani yelled, glaring at him with the kind of passion the Doctor always appreciated in his companions; Sarah Jane had certainly chosen well when bringing her group together…

"No, no, no, no, no, Rani, don't you see?" Sarah said, halting the younger woman's accusations as she looked at the Doctor, a slow smile spreading across her face as the Doctor looked back at her.

He might still wish he could have had longer with her in the TARDIS than the time he'd spent- if it hadn't been for his summons to Gallifrey he sometimes wondered how long they would have stayed together-, but even in a universe where the Faction were behind so many curtains it was hard to know what was going to remain a certainty from day to day, he knew that he could always count on Sarah Jane Smith.

"It's you, isn't it?" Sarah said, smiling as she looked at him in amused resignation. "Oh, you've done it again."

"Hello, Sarah Jane," the Doctor said, smiling warmly at her.

"Doctor?" Sarah said, apparently testing the waters, the Doctor allowing his reassuring smile to say everything she needed to hear in response.

"That's the Doctor?" Rani said, looking at him incredulously.

"What Doctor?" Jo said. "_The _Doctor? My Doctor?"

"Well, he can change his face," Sarah began.

"Well, I know, but into a baby's?" Jo asked (Not that the Doctor could blame her; his second and third incarnations had really looked rather similar in age, and the old man was just… well, _old_).

"Oi, imagine it from my point of view!" the Doctor countered (He automatically checked what he'd been about to say; from Jo's perspective that mess with the Tractites hadn't actually happened in the end, what with it all being erased from history and the slight detour he'd made to encourage Cliff to give her another shot in the pre-Paradox days). "Last time I saw you, Jo Grant, you were, what, twenty-one, twenty-two? It's like someone baked you."

Jo gasped in mock outrage- he might not have seen her regularly for centuries, but you couldn't spend three years in constant company with Jo Grant and _not _remember her expressions-, but further conversation was averted when the other boy- Jo's grandson Santiago, if the Doctor was remembering the family tree correctly- drew their attention to the approaching vulture-like creatures clad in long purple robes with white fur trim.

"Ah, yes," the Doctor said, walking through the group to stare at the new arrivals, "the Claw Shansheeth of the Fifteenth Funeral Fleet; I've been looking for you. Have you been telling people I'm dead?"

"I apologise," the Shansheeth replied in the tone of the voice that did little to convey sympathy. "The death notice was released a little too soon, though I can rectify this immediately!"

Before the Doctor could move out of the way, the Shansheeth had raised its hand and fired a red energy weapon of some sort at him, filling his body with an intense sensation of pain as he gasped from the shock, unable to do anything more than fall to his knees as the weapon continued to assault him, a vague comment the Shansheeth made about how they regretted his loss and he should 'rest in peace' only just audible as he tried to glare at them, refusing to let the weapon stop him…

Suddenly, everything around him seemed to glow, and the pain ceased, leaving him gasping on the ground at the sudden return of other sensations aside from agony.

"Doctor?" Amy suddenly said, her voice bringing the Doctor back to reality more than the loss of pain ever could have, prompting him to look up at her with a brief smile followed by an apologetic shrug as he noted their continued presence on the Crimson Heart's wastelands; evidently, considering the current device's dependence on his mental focus to establish the link to Clyde, the pain he was experiencing must have caused him to lose concentration and send him back here.

"Sorry, can't stop; I have to get this thing _working_," he said, turning his attention completely back to the device before him, the device now pulsing in a manner that put the Doctor in mind of a countdown; evidently the programming patch-job he'd used wasn't going to hold for long.

If he could just have some time to work on it with some more professional tools than his bare hands, he might be able to make this work…

"Back in a moment!" he said, activating the device once again to find himself running along a corridor after the rest of Sarah's group, Sarah standing in a door just as he ran through it.

"Come along, Smith!" he said, foregoing explanations in favour of escape as they ran along the corridor, until his eyes finally fell on a solid-looking door; considering that the Shansheeth could have only come this far with an insider in UNIT, it was urgent that he get Sarah and the others to safety before he tried anything else.

"In!" he yelled urgently, putting on a quick burst of speed to usher the group into the room ahead of him. "In! In! In! In!"

"I'm sorry," an impatient voice said as the last of Sarah's group ran through the door, prompting the Doctor to turn and look at a dark-skinned woman dressed in a military uniform, looking impatiently at him. "Is there a problem?"

For a moment, the Doctor thought about simply closing the door and ignoring the new arrival, but no sooner had he done so than he decided against it; in his experience, people were more non-plussed when faced with some kind of explanation than they were if you just did nothing.

"Sorry," he said, opening the door to look faintly apologetically at the woman on the other side. "I was… slamming it."

With that, he stepped inside the room and did what he had just said, slamming the door behind him before he turned to look at the others. "Right; now we need to lock it! Come on, use the sonic lipstick."

"Haven't you got the screwdriver?" Sarah asked, even as she stepped forward to do as he had instructed.

"Had to dismantle it; long story," the Doctor said, stepping away from the door to allow Sarah to do her job as he looked over at Jo with a smile. "Right then; sorry to be quick, but Amy needs us and we're running out of time, so Jo, Sarah, I need you."

"Need us for what?" Jo asked, looking at him with the same eager smile that had been her default expression back when they'd first travelled together, the smile that the Doctor had missed so much during his last meeting with her amid the other nightmares of the Tractites…

"Remember the old days when we'd go zooming off to faraway worlds?" the Doctor said, taking Sarah and Jo by the hands before he relaxed his mental link to the artron projector…


	20. Reflections of Past Companions

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Just to clarify, all scenes back on Earth with Clyde, Rani and Santiago will be the same as they were in the original episode, so they won't be appearing here directly

The History of Paradox

Amy still wasn't entirely clear what had just been happening. She'd understood that the Doctor had constructed the device with the hope of 'homing in' on Clyde's location, and she could guess that the device had swapped the Doctor with Clyde- Clyde himself actually seemed like he'd be interesting to talk to, even if they hadn't had the time to actually talk much amid Clyde's panic about what was happening to him-, but she wasn't entirely clear on how or why the device was still switching them back and forth, or how the Doctor had suddenly reappeared holding the hands of two women in their fifties, the women looking around at their surroundings in shock.

"Right," the Doctor said, releasing his grip on the womens' hands as he turned his attention to the device behind them, crouching down to pull various wires out of the machine that disabled its previous humming. "Now then, let's get you working properly…"

"Where are we?" the blonde-haired woman asked, looking at the Doctor and the other woman in confusion.

"The Doctor called it the Wasteland of the Crimson Heart," Amy said, just as the Doctor's device finally stopped pulsing, drawing their attention to her at last.

"Planet Earth's that way," the Doctor said, standing up from the machine to indicate a point in the sky behind Amy. "Bit of a long walk- sonic, please!"

"Wow!" the blonde woman said, her expression a shocked sense of joy at the sight before them. "Oh, so many years since I was on another planet…"

"Me too," the brunette woman said, smiling at the sight of the red landscape and strange sky, pausing only to hand the Doctor a small device with a red light on the tip that Amy assumed was the 'sonic lipstick' he mentioned he'd given to one of his old friends, before she focused her attention on Amy. "Who are you?"

"Amelia Pond, but call me Amy; almost everyone does," Amy said, holding out a hand and smiling politely at the older woman. "I'm… well, I _will _travel with him."

"You 'will'?" the brunette repeated, looking at the Doctor with a quizzical smile even as she shook Amy's hand. "I somehow doubt you live here normally…"

"I'm giving Amy the occasional trip to other worlds while she's on her school holidays, but full-time companionship is on hold until she's finished school; make sure she's prepared, you know," the Doctor explained with a smile. "I was seven years late helping her deal with a crack in time and space in her wall, I think she'll be good company… it's a whole thing."

"Ah," the brunette said, nodding at the Doctor before she smiled over at Amy, stuck for anything else to say. "Well… nice to meet you."

"Thanks," Amy said, smiling back at them. "So… you're Sarah Jane Smith? The Doctor said that you would probably be with Clyde when he found him…"

"That's me," Sarah said, smiling at the young redhead.

"Jo Jones," the blond woman added, smiling warmly at the young girl as she stepped forward to offer Amy her own hand. "I travelled with the Doctor too-"

"Before her, right?" Amy asked, briefly indicating Sarah as she smiled warmly at the other woman. "He told me about you both."

"Really?" Jo said, looking at the Doctor with a slightly uncertain smile on her face, as though she wasn't sure how to respond to that news.

"We've had a lot of time and I want to make sure that she's ready for whatever we might run into; that involves sharing some old stories with her," the Doctor said with a shrug, before he turned his attention back to the device in front of him in a manner that was just 'Doctor-ish' from him even if it would have been rude from anyone else. "We need to keep moving; I need to recalibrate this thing if it's going to work properly for a long-range permanent switch, and Clyde, Rani and… Santiago, right?... will need help back home sooner rather than later," he continued, looking briefly over at Jo for confirmation about the boy's name before he turned his attention back to Sarah even as he continued to work at the device. "By the way, forgot to ask; was the UNIT official who told you about my funeral an Indian-looking woman with long dark hair?"

"Yes; Colonel Karim," Sarah confirmed.

"Oh, good," the Doctor said, smiling in relief. "I had enough trouble with Mike being used against me the last time someone tried to infiltrate UNIT; at least now I can feel more comfortable assuming that it's someone who _doesn't _know me."

"Someone _betrayed_ you?" Amy asked, looking at the Doctor in surprise.

"It was a long time ago and he'd been through a lot before he got to that point; he's more than made up for it since then," Sarah said, looking firmly at Amy, a similar stare of firm resolution on Jo's face.

After a moment's awkward silence, the Doctor continuing his work while the other three were left uncertain what to say to each other, sitting around the device out of a lack of anything else to do- Amy, for one, had no idea what she could say to the Doctor's past companions that wouldn't end up coming out the wrong way-, but Sarah finally broke the silence as she walked over to crouch down beside the Time Lord.

"Did it hurt?" she asked, looking uncertainly at the Doctor as he moved a few cables around on the machine, her voice lowering as though she didn't want Amy to hear what she was saying. "The regeneration, I mean. That last body of yours… was he OK, in the end?"

"It always hurts," the Doctor said, after a moment's pause, as though deciding whether or not to answer that question, the brief tone making it clear he wasn't going to take that conversation any further.

"So… how did you end up here?" Sarah asked; evidently, she was just as eager as Amy was to end the awkward silence that had settled over them.

"The Shansheeth lured us in with a signal of some sort- I was passing by trying to find something interesting for Amy's next trip-, and… well, mighty old battlefield, just begging to be explored; couldn't resist," the Doctor replied with a slightly embarrassed smile.

"Trip?" Jo asked, looking curiously at Amy.

"He takes me on a trip or two during the holidays if I did well at school, and the rest of the time we talk a bit about what's out there and what I'm doing at school," Amy explained, before she indicated the machine that the Doctor was currently working on. "Anyway, the Shansheeth stole the TARDIS and he had to put that together out of whatever he could find here to get us back to Earth, and… well, here we are."

"He was always doing that back when we were working together at UNIT; we'd be stuck in a building trapped in a time field and he'd whip up something to shut it down with a few random objects," Jo said, smiling briefly over at Amy before she looked at the Doctor with a suddenly uncomfortable expression. "Did you ever… think it was stupid of me to leave when I did?"

* * *

><p>"Eh?" the Doctor asked, looking over at his old companion curiously, thoughts on his current task forgotten as he looked at Jo (He didn't want to think too much about how much older she looked now; this was why he always felt so uncomfortable meeting old friends, who kept on aging when he seemed to be gaining increasingly younger bodies…).<p>

"Well, I only left because I was getting married, and now… well, here you are, training someone specifically to become your companion, and I just decided to leave after all the time you spent teaching me as a scientist…" the blonde woman said, her tone awkward as she spoke to the man who looked like he should have been her son rather than the teacher her words implied. "Must've seemed a bit dumb, I suppose…"

"Why would you ever think I thought that?" the Doctor asked, pausing in his work to look sympathetically at Jo.

"We'd been travelling down the Amazon for months," Jo explained, as the Doctor walked over to sit down beside her, ignoring the curious looks he was receiving from Sarah and Amy as he focused on his former assistant, "and we reached a village in Cristalino, and it was the only place in thousands of miles that had a telephone, so I called you- I just wanted to say hello-, and they told me that… you'd left."

The Doctor simply sat in silence, listening to her story as Amy and Sarah looked on, Sarah remembering her own role in the Doctor's departure during the events described while Amy was left with an uncomfortable feeling that she might be witnessing her own future (The Doctor would have to talk with her about that; Jo's story was accurate, but she had made the decision to leave, after all).

"You left UNIT and never came back," Jo said, her voice trembling slightly, the Doctor unable to do anything but listen to her speak. "So I waited, and waited, because you said you'd see me again. You did, I asked you, and you said yes, you promised…"

Under other circumstances, the Doctor would have been grateful to know that the Tractite encounter had been erased from history- that had not been a pleasant experience for any concerned party, even if the resolution had been the best that could have been managed in such a situation, but what Jo had done during that time still haunted him-, but right now he was just focusing on the dejection on the face of the woman he'd once considered a daughter…

"So I thought," Jo continued, a slight trace of a tearful tremor in her voice as she continued, "one day, I'd hear that sound… deep in the jungle, I'd hear that funny wheezing noise, and a big blue box, right in the middle of the rainforest… 'cause he wouldn't just leave, not forever… not _me_…"

The Doctor could only smile at that statement; it might have been years since those old days at UNIT, but Jo remained a close and dear friend…

"I've waited my whole silly life…" Jo said, smiling and sobbing as she raised a tissue to her face.

"Oh, but you're an idiot," the Doctor said, attracting an incredulous stare from Amy even as his attention remained focused on Jo.

"Well, there we have it!" Jo said, throwing up her arms with a shaky sob.

"No, but don't you see; how could I ever _find _you?" the Doctor said, cutting her off before she could get started on another mournful rant. "You've spent the past forty years living in huts, climbing up trees, tearing down barricades… You've done everything from flying kites on Kilimanjaro to sailing down the Yangtze in a tea chest; not even the TARDIS could pin you down!"

"Hold on…" Jo said, her earlier shaky sobs fading as she looked at him with greater curiosity. "I _did _sail down the Yangtze in a tea chest… how did you know?"

"And that family!" the Doctor said, smiling wistfully at the memory of his brief hop into Jo's relative future. "All seven kids, twelve grandchildren, thirteenth on his way- he's dyslexic, but that'll be fine, great swimmer…"

"So… you've been watching me?" Jo asked, looking at him with a new smile about her manner. "All this time?"

"No," the Doctor replied, becoming more solemn without really thinking about it. "Because you're right, I don't look back; I can't… especially not _now_…"

He knew that his grim stare was attracting attention, but he'd tolerate that in place of having to answer awkward questions; he couldn't drop in on his old friends too often now without attracting too much attention to them specifically.

Even if the Faction probably already knew most of his old companions thanks to the Grandfather, he knew that the Doctor didn't like to look back on old friends unless he had to; this was no different…

"But the last time I was dying," he continued, allowing his expression to brighten at the recollection of his prior self's last indulgence, "I looked back on all of you. Every single one. And I was so proud…"

It had been risky for so many reasons, but with the radiation contaminating his temporal signature, he'd felt that it was as good a time as any to confirm that they were all safe; Ben and Polly running their orphanage, Ian and Barbara elevated from local school teachers to lecturers at Oxford, Tegan fighting for native rights- and cured of that tumour thanks to his little warning; a slight paradox, but considering that she'd still had enough of a tumour to merit surgery it was just bending the rules rather than breaking them-, Peri still travelling, Sam's campaigns…

"It really is you, isn't it?" Jo said, looking at him with a joyful smile amid her sobs.

"Hello," the Doctor replied, smiling warmly at the blonde, before a shrill whistle brought them back to the other matter.

"Sorry," Sarah said, lowering her whistle as she looked at them, "but we've got that lot back at home with the Shansheeth!"

"Yes!" the Doctor said, getting back up and walking over to the device. "And I still need you, Jo; that back of yours, I can smell blackcurrant. Is it buchu oil?"

"Hand-picked in Mozambique," Jo replied, following the Time Lord as she removed the item in question from her bag.

"Perfect!" the Doctor said, grinning as he took the small bottle from her. "These circuits need connectivity…"

After a few moments of shaking the small bottle of oil into the top of the device, he screwed the top back on and grinned at his old friends. "That's it! Intergalactic molecular streaming with just a hint of blackcurrant!"

"It's ready?" Amy asked, looking at him with an enthusiastic smile.

"Completely!" the Doctor confirmed, looking over at Sarah and Jo. "What a team! Come on, come on, time to get home!"

"But what about Clyde?" Sarah asked, looking in a slightly pointed manner at the Doctor.

"No, no, I've fixed it; blackcurrant juice acted as a connection matrix to fill in the gaps," the Doctor explained with a smile. "With the extra conductivity provided by the blackcurrant, we can utilise the intergalactic molecular streaming system with Clyde as the target rather than one of the subjects; we go home and Clyde stays where he is."

"That simple, eh?" Amy said with a smile.

"It's fiendishly complicated, actually, but time to worry about that later," the Doctor said, taking Sarah and Jo's arms once again before Amy hurried over to wrap her own arms around the Doctor's waist. "Just… hold on tight…"


	21. The Memory Weave

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: To confirm for all concerned, the scenes with Clyde, Rani and Santiago being trapped and the Doctor rescuing them are the same as they were originally; I'll be focusing on what's changed

The History of Paradox

After the sensation of blue surrounding them had passed, Amy opened her eyes to find herself standing in a basic-looking corridor that put her in mind of Poseidon Eight.

"We're on Earth?" she asked, looking over at the Doctor.

"We're on Earth," the Time Lord confirmed, s Amy smiled broadly in relief; at _last _something was going their way…

"Get us out of here!" a voice said from a nearby vent, ruining the moment.

"Oops," the Doctor said, hurrying over to examine the vent where the noise had come from. "Then again, maybe leaving Clyde in the same place wasn't such a good idea…"

"Look out; stand back!" Sarah said, pulling out the sonic lipstick and aiming it at the corners of the vent with a brief zapping sound, the Doctor effortlessly lifting the cover out of the way.

"Ah, ventilation shafts!" he said, grinning as he stared at the now-open tunnel before giving Sarah a brief nudge. "This takes me back… or even forwards…"

"Hurry up!" a voice that Amy vaguely recognised as Clyde's yelled up from the other end of the tunnel as the Doctor climbed into the vent. "We're getting boiled alive!"

"Hold on!" the Doctor yelled, as he advanced further into the tunnel. "We're coming!"

Amy was just about to follow her friend when something grabbed her by the arm and hauled her away from the vent, leaving her looking at a creature that reminded her of a purple-robed vulture before it grabbed Sarah and Jo and began to walk away. Amy tried to call for help at first, but quickly stopped herself; they weren't in any immediate danger right now, and Clyde and his friends definitely needed the Doctor's help.

It had been one of the harsher lessons that the Doctor had given her, even if it had been intended for the opposite situation; if she had to make a choice between saving civilians or saving the Doctor, focus on saving the civilians and have faith that the Doctor could look after himself.

She hated the lesson- leaving the Doctor in danger felt _wrong_-, but she had to agree with the point; with the training she'd received from the Doctor over the years, she was better equipped to handle whatever she might be about to deal with, but it sounded like Clyde and his friends needed the Doctor's help to get out of whatever problem they were in, while they weren't actually in any obvious danger yet.

Trying to look more comfortable than she felt as she, Sarah and Jo were marched along the corridors- she might be the youngest person here, but she wasn't going to be the weak link-, Amy held her head high and glared at the vulture-like aliens around her when she could, until they came to a larger room with a couple of benches in front of a large blue curtain. Amy's attention was immediately drawn to a tall, dark-skinned woman with long dark hair under a red cap, casually walking away from a computer monitor.

"I never trusted you, Colonel, from the moment I met you!" Sarah spat, which at least confirmed that this woman was the traitor they'd been discussing earlier.

"Like I care," the woman said, looking contemptuously back at Sarah. "Frankly, I've never met anyone so staggeringly pious in all my life."

"At least she _cares_," Amy said, glaring up at the older woman. "You betrayed the man who's done _everything _for this planet-"

"Like attracting attention to it?" the woman asked, looking at Amy in a manner that reminded Amy of the psychiatrists she'd had to deal with before the Doctor returned to her life. "How many of the alien threats we've fought only came here because _he _was here?"

"You're getting into _that_?" Amy asked, looking incredulously at the colonel.

"Maybe the _Master _only came here because of the Doctor, but that's hardly _his _fault!" Jo said, joining Amy's indignant glare.

"In any case, that doesn't matter right now," Karim said, waving a dismissive hand at the door behind them. "With the chamber sealed, the Doctor would need a ton of dynamite to get through that door, and we all know he never carries something like that anyway; too afraid of us to make it easier for himself-"

"'Us'?" Jo repeated, looking pointedly at Karim. "Who's 'us'?"

"You can't be referring to the Shansheeth- you're not that removed from the human race-, and they're not dangerous enough for the Doctor to be _that _afraid of them…" Sarah said, her expression thoughtful as she looked at the rogue colonel.

"What I meant was-" Karim began, rapidly turning to glare at the journalist.

"Oh God…" Amy said, her eyes widening in horror at the sight of a slight line around the edge of the colonel's face.

It wasn't a significant line, but with memories of Cousin Marion's face under his Oswald Fox 'mask' still clear in her mind regardless of how long it had been since that dark day on Poseidon Eight, Amy already knew what she, Sarah and Jo were facing.

"What?" Karim said, looking at Amy. "Is there something you'd like to say?"

"Just that your face looks a bit loose," Amy said, the comment slipping out before she could stop herself.

Reaching to the point that Amy was looking at, Karim sighed as her fingers made contact with the line, reached underneath it, and pulled the face off like those _Mission: Impossible _masks Amy had seen in the movies, revealing the withered features of a Faction agent underneath it.

To Amy's relief, Karim's true face only looked slightly older than her true appearance rather than the ridiculously ancient features of Marion- maybe that meant she wasn't as senior in the Faction or something like that-, but it was still enough for Amy to confirm that she was looking at another Cousin of Faction Paradox.

"Oh no…" Sarah said, looking at the colonel in horror before her expression became confused, eyes narrowed as though trying to recognise what was in front of her. "Hold on… do I…?"

"The malleability of history, Miss Smith," Karim said, looking over at Sarah with a mocking smile. "You were present at a moment that no longer exists in your timeline, but when it created a god…"

She chuckled maliciously. "Well, things become trickier to forget when they're _that _important, no matter what else happened."

"What are you talking about?" Sarah asked.

"He didn't tell you?" Karim said, smiling as her gaze shifted between Sarah and Amy. "Spending so much time with you, and he won't even reveal what makes him so determined to train you…"

"What are you talking about?" Jo asked.

"Later," Karim said, waving her hand dismissively. "We have other things to deal with now."

"The TARDIS!" Jo said, the blonde's words drawing Amy's attention to the familiar police box at the other end of the room that had briefly escaped her notice, along with a disturbingly organic-looking console and three long brown things that put Amy in mind of a straightened dentist's chair. "I never thought I'd see it again!"

"That's what this is all about," Karim said, her tone smug with self-satisfaction as she looked over Jo and Sarah before her gaze settled on Amy. "The TARDIS, and you three; the girl was a nice little bonus, but making a third chair with the weave isn't that hard…"

"Place them in the memory weave," the Shansheeth proclaimed, as the three women were manhandled into the relevant chairs, held down by straps around their arms and legs and with a strange plastic-like headband around their heads, the headband topped with a metal rectangular box and blue and yellow alternating lights.

"Well, come on then!" Sarah said, glaring defiantly at the Shanshseeth. "Tell us! What exactly does a Memory Weave do?"

"'Cause I warn you, darling," Jo added, "the memory's going at my age!"

"You need remember only one thing," the Shansheeth proclaimed.

"Which is?" Amy asked, glaring up at the alien.

"The TARDIS key," the Shansheeth said, as it walked back to the control console.

"The Weave takes the memory out of your head, and makes it real," Karim explained, as she walked over to adjust the headband around Sarah's head, an eager grin on her face. "This device can build a physical key out of your thoughts… and then, we will have access to the TARDIS."

"NO!" Amy yelled, horror on her face at the mere thought of the Faction gaining access to the Doctor's ship.

The Doctor almost never spoke of the Faction- Amy had wanted to ask him for more information about his apparent history with them, but the look on his face whenever they came up had quickly discouraged her from pursuing that line of inquiry-, but she'd heard enough stories to have some idea of what they were capable of now, even if the Doctor had mentioned once or twice that their potential was still limited; if they acquired the power of the TARDIS, and everything that the Doctor's people had known about time travel…

"You can't do this!" Sarah yelled.

"We have seen so much death…" one of the Shansheeth said, his expression as solemn as a vulture could look. "The Shansheeth have presided over infinite funerals; we see the pain and the suffering, again and again and again… but with the TARDIS, we can stop this-!"

"And you think _she'll _help you do that?" Amy yelled, glaring over at Karim.

"This accomplishes my goals-" Karim said in a dismissive manner.

"And what are _those_?" Amy said, glaring at her.

"It is a noble quest," the Shansheeth said, in the fanatical tone of the insane that Amy had heard too often on the rare occasions when the Doctor had shown her some of the TARDIS's archived recordings of past journeys. "To halt the endless, endless weeping, and change the whole of history!"

"That's why creatures like you can't have time machines," Sarah said, voicing Amy's own thoughts as they both glared contemptuously at Karim. "Because you'll wreck the entire universe!"

"So pious…" Karim said, looking mockingly at Sarah. "The rules of the universe are what can be forged by those in power; if the Shansheeth have the power to make their mark, who are you to stand in their way? What makes your view any better than theirs?"

"Considering that all _you _get out of it is chaos, _every _right!" Amy said, glaring indignantly at Karim. "You just want to make the universe dance to your whim; you don't _care _about anything but yourself!"

"Accelerate the wave!" Karim said, ignoring Amy's protests as the girl suddenly found herself with a terrible headache, Jo and Sarah yelling in similar pain around her as she felt like something was digging into her brain…

"Amy!" a familiar voice yelled from outside the room's door, only just audible over the other noise. "Jo, Sarah, can you hear me?"

"They want the key!" Sarah called over to the door. "They've got the TARDIS and a memory weave!"

"Too late!" Karim said, looking over at the door before looking back at the Shansheeth. "Full activation!"

"Concentrate!" the Shansheeth proclaimed, apparently unconcerned about the Doctor's arrival. "Think of the key!"

As Amy looked over at Jo and Sarah, she wished that she could escape the feeling of something burrowing into her mind, rifling through what should have been private to dig up what they wanted…

"I've got the original!" the Doctor yelled through the door. "You can have it if you let them go!"

"You let the Doctor inside this room and he will destroy us," Karim said (Amy supposed she should have expected that, a UNIT captain who was affiliated with the Faction was obviously not going to underestimate the Doctor). "Keep going."

As the memory weave continued to hum, Amy found herself increasingly unable to think of anything other than the time she'd spent in the TARDIS with the Doctor, all the times he'd opened the door to allow her to witness the small universe that had been his home for so long…

"Fight it!" Jo said, looking urgently between Amy and Sarah. "Try to think of something else!"

"I can't!" Sarah yelled.

"Neither can I!" Jo admitted.

"Me neither!" Amy screamed, her memories suddenly filled with all the times she'd studied her TARDIS key when she was home alone in bed after her latest lessons with the Doctor, the times she'd looked around the ship…

"The memories coalesce!" the Shansheeth proclaimed, as some kind of strange golden energy that reminded Amy of what the Doctor had expelled when she'd first seen him emerged from the headbands, colliding between the three of them to form some kind of strange ball. "The key takes shape!"

"No!" Amy protested, her mind continuing to replay memories she didn't want, Jo and Sarah's own denials only just audible over her own refusal…

"Sarah, Jo, Amy!" the Doctor's voice suddenly yelled once more, this time apparently over a radio rather than through the door. "Can you hear me?"

"The key!" Sarah gasped. "It's almost ready!"

"Listen to me," the Doctor said, his tone firm and controlled. "I want you to remember."

"We are!" Jo said, her body shaking as the weave continued its work. "That's the trouble!"

"No, no, no, no, no," the Doctor corrected. "I want you to remember everything."

Amy wasn't sure if it was her own experience with this Doctor- he'd mentioned regeneration to her once or twice, but mainly as a means of explaining his odd behaviour when they'd first met; all she really _knew _was that he changed shape when he was badly injured-, but she knew what he was planning even before he continued to speak.

"Every single day with me; every single second…" her friend continued, as Karim looked at the Shansheeth in confusion. "Your memories are more powerful than anything else on this planet right now; just think of it, Sarah, remember it, Jo, and imagine it, Amy, but give them _everything_! Every planet, every face, every madman, every loss, every sunset, every terror, every joy, every Doctor… _everything_."

Amy didn't have much personal experience to draw on, but as she focused hard on her memories of her visits to Ember, Poseidon Eight, and Metebelis Three, and her first encounter with the Atraxi and Prisoner Zero, she also drew on the memories of the stories the Doctor had told her about so many of his past experiences, the wonder he'd felt at witnessing the Selachian homeworld, the incredible concept of Avalon, his time among the higher dimensions…

Amy vaguely heard additional voices from outside talking to Jo and Sarah, but they were barely audible over Karim's screams of protest as the memory weave began to fall apart, the system sparking as the energy-key forming between them began to disperse, the Faction member's pleas for the key to be brought back irrelevant as Amy let the memories come forward once more…

"_Weave starting to self-destruct_," a computerised voice said, just as the bonds holding Amy and the older women to the machine suddenly released their grip. Not wasting any time, Amy shoved her headband off and joined Jo and Sarah as they hurried over to the door, the Shansheeth and Karim trapped on the other side of the room by the exploding console…

"Doctor!" Amy yelled, anxiously slamming her hand against the door as Sarah's attempt to use her sonic lipstick on the lock met with failure. "We're safe; open this door!"

"I can't open it," the Doctor said, a resigned tone to his voice as he relayed that information to them. "No sonic screwdriver; it's been dismantled."

"And we can't get in because we stopped ourselves getting the key…" Sarah finished for him.

"I just want to say," Jo said, walking up to the door to address the group on the other side, "I'm so glad I saw you again. I waited all this time… and it was worth it, every second."

She smiled slightly morbidly. "Funny thing is, your funeral turns out to be ours instead-"

"_Funeral_!" the Doctor suddenly yelled. "That's IT!"

"What's it?" Amy asked.

"Don't you see?" the Doctor called through the door. "It's my funeral, with a _lead-lined coffin_!"

Amy didn't need any further advice to realise what the Doctor was talking about; with the Shansheeth and Karim still stuck on the wrong side of the room, the three of them ran for the coffin, ignoring the deep-voiced countdown from the other side of the door as they raised the lid open before diving in to the large box, Sarah and Jo on either side of Amy with their arms wrapped around the smaller figure after pulling the lid shut above them.

For a few moments after the last explosion had faded from their ears, the three of them simply lay in the box in silence, unwilling to open it and see what had happened around them, until the lid was raised once more to reveal the Doctor standing over them, grinning broadly, a dark-skinned girl and Clyde to his right.

"There you are!" the Doctor said with a satisfied grin. "Smith, Jones and Pond!"

"DOCTOR!" Amy said, leaping from the coffin to throw her arms around him, Jo and Sarah climbing out of the coffin after her with relieved smiles.

"Sarah Jane!" Clyde Langer's voice yelled out, prompting Amy to look up from the Doctor's shoulder to look at the dark-skinned young man now enthusiastically hugging Sarah, along with the previously-noticed girl, while a taller boy with paler skin and dark hair hurried over to Jo.

"Santiago!" Jo said, grinning as she hugged the other boy.

"It's so great to see you again, Gran!" Santiago said, looking back at her in relief before he looked over at Amy as she released her grip on the Doctor and turned to look at him. "And you're…?"

"Amy Pond," Amy said with a smile, walking over to shake Santiago's hand before she indicated the Doctor. "I'm with him."

The sound of an unusual groan prompted Amy to glance around the room, before her eyes fell on what appeared to be Colonel Karim's body and then immediately wished she hadn't. Despite having been exposed to fire powerful enough to destroy virtually everything else in the room, Karim's body was still moving, looking up at them with a bitter glare even as she lay amid the ruined bodies of her former Shansheeth allies, her face even more twisted and withered than it had been when she'd removed her mask earlier.

"Doctor…" she said, glaring up at the Time Lord with a cold stare. "You think you've won…?"

"I think I've stopped this," the Doctor said, looking coldly at the former UNIT colonel, the others taking a step back to give the Time Lord a chance to talk. "As to everything else, your Faction is not going to get the TARDIS; I'd tell you to tell that to the Grandfather, but you're not going to be around long enough to deliver the message."

Karim glared weakly at the Doctor for a moment, before she collapsed to the ground and lay still, leaving her enemies staring grimly at her body.

"So…" Sarah said, looking curiously at the Doctor. "She was with… the Faction?"

"Yes," the Doctor said, looking solemnly at Sarah. "They've been… expanding their resources lately."

"The Faction?" Jo asked.

"Time-travelling voodooists who believe that time is irrelevant as a structure and there's nothing to reality but whatever they want to believe," the Doctor said, his expression solemn as he stared at the body. "They can only do so much without damaging Time itself, but what they can do is still dangerous enough…"

Stuck for anything else to do in the face of her friend's solemn expression, Amy reached over and squeezed his hand affectionately, prompting the Doctor to turn and smile back at her before he looked at the rest of the group around him.

"Right then," the Time Lord said, grinning at the group of people around him in a manner that made it clear he didn't want to discuss what had just happened in more depth, "I'll just… get you home, shall I?"

* * *

><p>"Same old TARDIS," Jo said, looking at the console room with a warm smile as Clyde, Rani and Santiago walked out of the ship as it reached their destination, the short trip having been dominated by the younger visitors looking around the TARDIS before it stopped and the Doctor opened the doors (Clyde and Rani had seen it before and Santiago had essentially stared himself out during the trip). "It doesn't matter what's changed, it still… <em>smells <em>the same."

Amy could only look at Jo with a smile at this news; even after so many years since she had departed the time machine, the idea that this woman could still look fondly back at the time they'd spent together…

"No!" Jo said firmly, opening her eyes and looking around herself. "Got to say goodbye, or else I'd stay with you forever. Besides, I probably couldn't keep up any more; get you into trouble with the Time Lords."

"Yeah…" the Doctor said, turning his attention back to the console. "I'd probably better go. You know me, stuff to do, Amy's still got school, things like that…"

"It's daft, though," Sarah said, exchanging a glance with Jo before looking back at the Doctor. "We were both saying, we had this theory that, if you ever died… we'd feel it, somehow; we'd just know?"

As much as Amy didn't like to think about it, she understood what Sarah was saying; the universe just couldn't go on as normal if the Doctor ceased to be…

"But that's just silly, isn't it?" Sarah said with a slight shrug.

"I don't know," the Doctor said, looking back at her with a solemn expression. "Maybe not. 'Cause, between you and me, if that day ever comes… I think the whole universe might just shiver."

After a brief silence, the Doctor made a move as though he was about to jump at them, and the moment passed, the Doctor walking up to give Jo a hug as Sarah laughed, Amy watching from the side with a broad grin.

"Well," Jo said, stepping back as she looked at the Doctor, "hopefully, if that moment does come, it won't be for a _very _long time."

"Amen to that," Amy said with a grin of her own (Anything to take her away from _that _morbid thought…).

"Just one thing," Sarah said, looking back at the Doctor even as she turned towards the door. "Don't we need to worry about the Shansheeth?"

"Unlikely," the Doctor said, indicating a screen on the TARDIS console. "They were most likely a rogue element; I've already intercepted an apology from the High Shansheeth Nest about their actions that they sent to your computer. I'm not saying you don't need to worry about them again, but there's nothing to suggest that they'll try this any time soon."

"Good," Sarah said, smiling at the Doctor before she looked at the youngest current resident of the TARDIS. "It was… lovely to meet you, Amy; hope you enjoy your time with him."

"I will," Amy said, grinning back at the older woman before Sarah impulsively bent over to give her a hug, Amy returning it out of a lack of anything else to do.

"Be safe," Sarah said, smiling at the red-headed girl. "The one thing he's always needed is a friend… and I think you'll be a good one."

"I will," Amy said again, looking solemnly back at the older woman before she and Jo left the TARDIS, leaving Amy and the Doctor alone in the ship once more.

"So," the Doctor said, looking at Amy with an apologetic smile, "sorry that wasn't as smooth as I promised…"

"Are you joking?" Amy said, looking at him with a satisfied smile. "We stopped alien vultures stealing the TARDIS and I got to meet some of your old friends; that was _great_!"

"And we saw the Faction," the Doctor pointed out, his expression grim at that reminder of their recent encounter. "It might have been only one agent, but we don't know what she shared with them…"

"We'll worry about that later," Amy said, reaching out to place a reassuring hand on his arm. "We stopped them now; that's all that matters."

Even as the Doctor smiled thankfully back at her while setting the ship's controls for her home time, Amy didn't need her long experience with him to see the edge of apprehension in his eyes; they might have come through this encounter, but there were still other elements of the Faction out there that could be a problem…

* * *

><p>AN 2: Hope you all liked that; a bit of a more straightforward reunion next time, as the Doctor takes Amy to see another old friend…<p> 


	22. Dinner with the Queen

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Another jump forward, this one featuring an audio companion, which I hope will meet with your approval despite its brevity; we're coming up to a particular set of events, and I thought the Doctor and Amy could do with a break before getting into that…

The History of Paradox

"Here we are!" the Doctor said, grinning as he opened the doors to reveal an underground cavern, well-formed but clearly very old, lit by various fiery torches that managed to provide a comforting sense of illumination along with adding a surprisingly comforting atmosphere to the location.

"Where are we?" Amy asked, as she walked out of the ship after her friend.

"The planet Peladon," the Doctor said, grinning proudly as he looked at Amy. "After Earth, it's one of my favourites; a rich cultural history with some very friendly inhabitants… although I'd recommend you call yourself a princess if anyone asks; they were relaxing about those rules last time I was here, but never hurts to be prepared."

"Right…" Amy said, looking uncertainly at the Doctor; he'd told her that he had something interesting in mind, but this seemed a bit basic for the engaging trip he'd promised. "And… why are we here?"

"Well…" the Doctor said, looking at her with a slightly awkward grin, "after the mess we ran into at our last stop, I thought you'd appreciate somewhere where I can guarantee that you won't be disturbed, so I thought here would be a good choice; it's at a relatively peaceful state of affairs right now, and I know a few people in the right places."

Amy was about to ask who those were, but the Doctor didn't even give her a chance to ask the question instead walking along the corridor with a confidence about him that left Amy with no real other option but to follow him. After a period of walking along corridors that were so complicated Amy had no idea how anyone could find their way around this place, they finally approached a larger door with an elaborate purple curtain draped over it, with two men standing outside in some kind of strange armour that Amy didn't recognise.

"Just dropping in; no need to announce me," the Doctor said, pulling out the psychic paper and flashing it briefly at the guards before putting it back in his pocket and walking through the door, Amy sticking close behind him out of a lack of anything else for her to do.

As they entered the room on the other side, Amy found herself looking at what could only be a throne, a tall woman sitting in it dressed in long purple robes. She had dark skin that suggested at a long time in the sun and close-cropped dark hair, cut in a style that reminded Amy of the traditional image of Cleopatra in history books, and was looking at the two new arrivals in an imperial manner.

"Who are you?" she said, a slight accent to her tone that Amy felt like she should recognise. "What are you doing here?"

"Hello, Erimem," the Doctor said, grinning as he looked at the woman despite the stare she was giving him in return.

"What?" the woman said, looking pointedly at him, her glare intensifying as she stared at the Time Lord. "Who are you?"

"I'm the Doctor," the Doctor said, still grinning at her, evidently unconcerned about her reaction to him.

"The Doctor?" the woman who was apparently called Erimem repeated, looking at him incredulously.

"Come on, you're Peladon's Queen; don't tell me you never looked up the stories about my previous visits?" the Doctor said, grinning broadly at her. "I had white hair and wore velvet on my first couple of visits, and I was definitely shorter the third time; you'd think all that would make it pretty clear that I'm not always the fair-haired fellow you knew."

"…Doctor?" Erimem said, her initial confusion forgotten as she continued to stare him, a smile broadening on her face as she looked at him.

"In the flesh," the Doctor said, grinning at her. "Good to see you, Erimem."

"It… I feel the same," Erimem said, giving him a brief warm smile before assuming a more serious expression once again- Amy thought she'd seen Erimem move as though about to hug him before stopping herself- as she looked at Amy. "And who is your friend?"

"Erimem, this is Amelia Pond; she's my current companion," the Doctor said, placing a warm hand on Amy's shoulder. "Amy, this is Erimem; one-time pharaoh back in Ancient Egypt, current Queen of Peladon."

"I see," Erimem said, nodding at her as she held out her hand, Amy awkwardly shaking it out of a lack of any other ideas what she could do with it. "It is a pleasure to meet you, Amelia Pond."

"Uh… same to you?" Amy said at last, smiling back at her (She wished she sounded more confident, but what could you say to a queen?). "And… call me Amy."

"I will," Erimem said, nodding at Amy before turning her attention to the Doctor. "Why are you here?"

"Nothing major, I promise; just wanted to show Amy something calm and interesting for a change, and thought this was a good place to do it," the Doctor said, indicating the throne room with a smile. "What can I say; it's been a few centuries since I came here, but I've always liked Peladon."

"That is good to hear," Erimem said, smiling at the Doctor before she looked back at Amy. "In any case, it is dinner soon, and with Pelleas and Alpha away on negotiations, I would have been dining alone, unless you care to join me before I show you around?"

"Dinner with the queen?" the Doctor said, grinning at Erimem. "How can we refuse?"

Amy could only nod eagerly in agreement, her broad grin saying everything that needed to be said as Erimem stood up and led the two of them to a small dining area a short walk from the throne room.

"This is it?" the Doctor asked, looking at Erimem in surprise as they entered the room. "Nice, I know, but… well, isn't it a bit small?"

"And quiet?" Amy added, looking uncertainly at Erimem. "I mean, you seem like a nice person, but I thought queens should… well, shouldn't you have guards?"

"We are deep within the palace, Amy; there is little need for guards this far in, and my people respect my privacy," Erimem explained, smiling at the girl before she looked at the Doctor. "As for the room we are in, this is the private royal dining hall, for those occasions when we wish to converse about personal matters among ourselves; the only way in is through the route we have just taken, or through the caves."

"Caves?" the Doctor said, a grin spreading across his face as he looked over at the other door in the room. "You mean… my _other _old friend is down there?"

"One of them, at least," Erimem confirmed with a smile, just before the door opened and a creature shuffled in that put Amy in mind of a furry warthog with a rhino-like horn and sharp teeth in place of tusks. The casual smiles on the Doctor and Erimem's faces at least suggested that she wasn't looking at anything dangerous, but Amy wasn't entirely comfortable being in a room with something that large even before it walked over to her.

"What-?!" Amy said, jumping in shock as the creature nuzzled at her, actually sounding like it was laughing as it rubbed its nose against her leg, Amy frozen from the shock after its initial appearance.

"It's all right!" the Doctor said, a reassuring hand on Amy's shoulder as he grinned at her before crouching down to stroke at the large creature's nose, grinning as he did so. "There you are, old boy… how are you, mmm?"

"Aggedor continues to flourish, Doctor," Erimem said, nodding at the Doctor with a smile. "She and her cubs are safe in the caves beneath the palace, and some of them- such as this one- have taken to coming up here when we eat."

"Sneaking a few table scraps, eh?" the Doctor said, the grin still on his face as he reached over to scratch the Aggedor behind the ears before looking over at Amy. "Amy, this is Aggedor, the sacred beast of Peladon; I made friends with this one's parents a few lives back, and they remain very nice company when they're needed."

Stuck for anything else to do, Amy reached out to touch the Aggedor's fur, her hand shaking slightly as she stroked it at first, but gradually relaxing more and more as the creature sat before her, grumbling in pleasure at her movements.

"Lot tamer than they were, aren't they?" the Doctor said, looking curiously at Erimem.

"It has to do with us being there when they were born, I believe," Erimem said. "They have come to recognise that we are their friends more easily than the Aggedors of the past, and they are thus more accepting of us."

"Wow…" Amy said, still staring at the creature, which was increasingly appearing less and less scary and more and more like a large puppy. "It's… it's _incredible_…"

"In so many ways," the Doctor agreed, smiling warmly at Amy as she sat alongside the Aggedor, crouching down to join her. "I thought the last Aggedor did helping me save Peladon's queen on my second visit, and then I found this one's mother on my third visit- fourth chronologically for Peladon, but that's another story-, ready to give birth after a century-long pregnancy to a new litter…"

"It was a new age for Peladon in so many ways, Doctor," Erimem said, looking warmly at her friend before turning her attention back to the table before them. "In any case, take your seats; we shall be served soon."

As they sat down around the table, Amy still occasionally stroking the Aggedor now curled up at her feet, the Doctor and Erimem fell into discussion about various parts of Peladonian society as the food was brought in, Amy occasionally asking questions when she felt like she understood something but otherwise savouring the unique foods and the equally-unique company before her.

She might not fully follow what her friend was talking about with his friend right now, but she was on a different planet faced with a highly unique creature while having dinner with a queen; what _wasn't _cool about that?

* * *

><p>AN 2: Short, I know, but I felt it appropriate as a 'calm before the storm' moment, as next chapter will see the Doctor and Amy deal with a threat a BIT closer to home...<p> 


	23. The Alien Mermaid

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: With this particular jump forwards, we find ourselves in the Easter holidays of 2006, where- based approximately on the canonical timeline- a VERY particular event is about to take place…

AN 2: Without giving away too much too soon, the villains' actions will be mostly the same as they were in the original course of events; naturally things will only start to diverge for the villains when the Doctor actually meets them face-to-face.

AN 3: Hope this works; it was surprisingly hard to adapt some parts of this story while exploring the differences between the Eleventh Doctor and the Doctor who was there originally…

The History of Paradox

Sitting on the Doctor's sofa as she stared idly at the television, Amy could only sigh as she casually flicked through the channels in front of her. With Aunt Sharon off on another trip and Rory's parents having taken him on holiday, Amy had taken advantage of the opportunity to spend a week in the Doctor's company, but he was apparently using the time to catch up with some work that needed done on the TARDIS. He'd let her into the house when she'd arrived, but after giving her a few books to read over as part of her lessons he'd gone back into the ship and heard nothing more from him apart from the occasional noise in e ship.

It wasn't that the books weren't interesting, of course- how many people her age got the chance to read about the cultural history of Mars and how it differed from the colony they'd established on New Mars in the aftermath?-, but she just wished that she could actually _go _somewhere again. Things had been so dull at school over the last few weeks- Rory was pleasant enough company, but he could only do so much for her, and Amy hated to think that he was limiting his own opportunities for her sake- that she just wanted a chance to go somewhere else, other than the monotonous appearance of Leadworth…

Stuck for any further ideas about where she could suggest for a trip, Amy flicked the TV over to another channel, only to find her eyes widening in shock as she watched the image on the screen before her; a large ship, obviously alien, flying through the air and crashing through Big Ben before coming to a rest in the Thames, all while the voice of a BBC news reporter relayed the news that the events she was witnessing had happened within the last hour.

She had no idea what had just happened, but she knew two things immediately; what she had just seen _was_ real, and that meant that she had to inform the one person on Earth best qualified to deal with it.

"_Doctor_!" she yelled, getting up and hurrying for the TARDIS door, practically tearing it open as she ran into the ship.

"What?" the Doctor said, pocking his head up from underneath the floor panel supporting the TARDIS console. "Amy, is something-?"

"An alien ship hit Big Ben!" Amy yelled, uncertain if she was excited or terrified at the thought of Earth coming in contact with aliens in her own lifetime.

"_What_?" the Doctor said, hurrying out of the TARDIS to look at the television screen, grabbing the remote to turn up the volume. Mayhem was visible on the streets all around the Thames as cameras focused on the vast smoking ship, which was shaped kind of like of a shovel but otherwise resembled nothing Amy had seen in her studies or travels so far, with the thoughtful expression on the Doctor's face suggesting that he didn't recognise it immediately either. So far the newsreaders were just reporting on the police reinforcements brought in to cope with the immediately resulting chaos, but there would be bound to be some kind of more definite response to the ship itself eventually…

"Right," the Doctor said, clapping his hands together after watching the television for a few moments, the displayed footage revealing nothing new other than that attempts to spot additional ships had so far met with failure, "I'll just take the TARDIS on a short hop to pick up Bessie and then we'll be off to London, Pond; in the meantime, you should get into something more… professional."

"Professional?" Amy repeated in confusion as she looked down at her clothing; she was only wearing a casual T-shirt and jeans, but the Doctor had never objected to her attire before now.

"Well, you'll be acting as my assistant when we get there; you need a shirt of some sort at least if we're going to get anyone to take you seriously," the Doctor said with a brief smile, before his eyes narrowed as he looked at the screen as it replayed the image of the crashing ship. "Besides, there's something not _quite _right about that…"

"There's not?" Amy said, her curiosity inspired even further by this news.

"Oh, it all looks good on a scientific level- what they've shown looks like a normal crash, angle of descent, colour of the smoke, all that stuff-, but crashing into Big Ben and landing in the Thames?" the Doctor said, looking sceptically at Amy as he indicated the screen that now displayed the half-submerged ship. "Doesn't that just seem like a bit _too _striking to be an accident to you?"

"You mean... they were trying too hard to be dramatic?" Amy asked, wanting to be sure she understood the Time Lord's explanation.

"Precisely," the Doctor said, his tone becoming increasingly grim. "So, we've got a genuine alien spaceship, arriving on Earth in the most theatrical manner possible, setting up a crash-landing that everyone can see; this could still be first contact, but I've got enough doubts to want to make sure…"

He shook his head solemnly before he looked at Amy once more. "As I said, get changed into something professional; I'll see what I can find out from the public channels- maybe make a call or two if time allows-, and then we'll be on our way."

Nodding in agreement, Amy hurried into the TARDIS, her goal to head directly for the ship's elaborate wardrobe, leaving the Doctor to continue his analysis of the available news reports as he stared intently at the television screen.

* * *

><p>A short while later, Amy was sitting alongside the Doctor in Bessie, the TARDIS parked in a London alleyway a short distance from their current position; the Time Lord had materialised his ship around the car to allow them to take it to London with them, subsequently taking a short hop after arriving in London to leave the car on the street while putting the TARDIS in a convenient spot. Amy had expressed her surprise at the Doctor's decision to take the car along, but her friend had insisted that it would be better for the moment if he limited any obvious signs of his true nature until they had a clearer idea what they were dealing with- particularly since some of his most immediately useful contacts were in other parts of the world at the moment-; his research had identified the hospital that the military were apparently using to examine the body of the ship's pilot, so they were going to check out that location as their first priority.<p>

The Doctor's decision to try and investigate this situation 'undercover' apparently only extended as far as making a few recommendations for what Amy should wear and not telling anyone in London that he was coming; what news reports he'd seen indicated that nobody he knew was in charge right now, and he didn't want to waste time telling strangers who he was until he had something to tell them. While the Doctor was still dressed in his usual tweed jacket, blue shirt and bow tie, and dark trousers, Amy had gone along with his suggestion and dressed up in a professional yet comfortable dark blue business skirt and trousers over a dark red shirt, putting her hair up in a bun to add to her more adult appearance. She felt that the hair gave her an older look, but it was hard to feel comfortable in this situation; she felt like she was trying to be something she wasn't…

"Just stay calm and look professionally impressed; look like you know what you're talking about, but don't look like you know too much," the Doctor said, looking firmly at her as he locked the TARDIS with a remote he'd added to the key before settling more comfortably into the driver's seat. "Remember, you're the assistant; you can't know too much about what we're looking into."

"I don't," Amy pointed out, a slightly exasperated yet fond smile on her face at the Doctor's faith in her.

"That's the spirit," the Doctor said, smiling as he turned around and started driving before Amy could say any more, the yellow roadster tearing through the streets with a speed that made Amy question his initial claims that he wanted to remain 'low-key' for a few moments until she decided to focus on maintaining a grip of her seat. After a few moments of rapid progress through the streets of London, weaving around other traffic while somehow avoiding even coming close to having an accident- Amy thought part of that might be because not many people were actually out and about right now, but this wasn't the time to analyse that issue-, Bessie came to an abrupt halt in front of a building Amy was only just able to identify as a hospital from a nearby sign before the Doctor leapt out of the car, leaving Amy with no choice but to follow him.

"Hello," the Doctor said as he walked up to the soldiers in front of the hospital doors, pulling out a wallet that wasn't his usual psychic paper and showing the contents to them. "Doctor John Smith, UNIT Scientific Advisor; I believe you have a situation in there that merits my attention."

"Doctor Smith?" one of the soldiers said, looking sceptically at the Time Lord. "General Asquith didn't-"

"I'm officially on leave at the moment, but I was in the area and thought I'd drop by to offer my services," the Doctor said, looking firmly at the other man. "Now then, if you don't mind, I believe there's something inside this hospital I should be taking a look at?"

"But-" the other soldier began, raising his gun to indicate Amy.

"Miss Pond is my personal assistant; I can assure you, she has full clearance and my complete confidence, and can unquestionably be trusted with knowledge of the contents of this facility," the Doctor said firmly. "Now then, are you going to let us in, or do I have to contact Sir Lethbridge-Stewart?"

The name appeared to be enough for the two men, as they virtually instantly lowered their weapons and stepped aside, allowing the Doctor and Amy to walk into the hospital, quickly following the signs to the morgue.

"So… what do we do when we get to this body?" Amy asked, after they'd been walking for a few moments. "Take it away?"

"First things first, I need to know what we're dealing with; what I saw of that ship gave me a few ideas about who might be responsible for this, but there's too many candidates for me to just identify them with what I know at the moment," the Doctor said. "After I've seen the body, we can decide-"

Further discussion was cut off when a scream filled the corridors, the Doctor not even needing to glance at Amy for confirmation before he started running towards the source of the scream, Amy hurrying along after them. As they rounded another corner, they encountered a group of soldiers coming from another direction, but a quick flash of the Doctor's psychic paper and him issuing orders about "Defence Pattern Delta!" prompted the soldiers to continue running with the Doctor and Amy alongside them. After a few moments' running, they charged into the hospital morgue, revealing a young Asian woman in a white doctor's coat trembling on the floor in a side room and an open door in what the Doctor recognised as a hospital storage unit (Waking up in one of those after his seventh regeneration had _not _been fun).

"It's alive!" the apparent doctor said, looking up at the new arrivals in shock as she cowered beneath a bench.

"Amy, stay with her!" the Doctor said, looking back at his companion before he looked at the soldiers; as much as he hated to admit it, when dealing with a potentially hostile life-form, the soldiers would be more practical than Amy, particularly given how young she was right now. "The rest of you, spread out; tell the perimeter it's a lock-down!"

"It's still alive…" the doctor whispered, apparently in shock as she stared at the door beyond her, Amy crouching down to place a comforting arm around the older woman's shoulders as the soldiers ran from the morgue to spread out around the hospital.

As Amy spoke soothingly to the doctor, trying to volunteer other explanations for the pilot's revival, the Doctor studied the morgue, but all three fell silent at the sound of something moving behind a table at the other end of the room. Looking warningly at the girls- considering the doctor's obvious terror, it was easiest if Amy stayed with her to limit the risk of panic-, the Doctor beckoned the remaining soldier standing at the door forward to join him- best to be prepared in this situation- before he slowly walked towards the table, crouching down as he did so; whatever this thing was, if it was moving about without being visible over the table, it was probably fairly short. After a few moments of careful progress, the Doctor peered around the corner of the desk…

A face peered out from around the corner of the desk, revealing the source of the sound to be what the Doctor could only think of as a pig in a spacesuit. It was clearly capable of moving on four legs, and it was wearing a black rubber-looking suit with a ring around the neck that suggested it had been wearing some kind of helmet earlier, but it merely grunted as it looked back at him in a very pig-like manner.

He'd been around the block more than once, and he'd seen some surprising-looking alien races that closely resembled Earth animals- the Menoptera were one race he'd always remember, and he still had a few theories about how the Onihr were related to the Judoon-, but he was fairly sure he'd never even heard of a race that looked like this.

"Hello," he said, smiling gently at the creature out of a lack of anything else to say, gently reaching out to it with one hand; he'd worry about the anomalies after he'd won this thing's trust. "Don't be afraid…"

For a moment, the pig looked at him in an almost curious manner, but then the sound of one of the soldier standing behind the Doctor re-arming his weapon startled it, causing it to turn around and run in the other direction, away from the Doctor, squealing/screaming as it ran, the Doctor scrambling to his feet to follow it…

The Doctor might have managed to stop his initial guard, but even with the pig-thing's stumpy legs, he didn't even have time to yell in protest before the pig ran around a corner and was shot by a soldier with a too-eager trigger finger, leaving it lying on the ground, snorting weakly as it stared up at the ceiling, clearly lost for what it could do, trottered hands reaching upwards.

Hurrying over to the body, the Doctor could only crouch down beside it and gently stroke its head as it died, staring coldly up at the soldier who'd just shot a terrified, innocent being that had been through something so horrible he couldn't believe anyone would do it; he might be able to understand why the incident had happened, but he was going to ensure that the other man knew he disapproved of it.

"_Think _next time," he said, looking firmly at the soldier standing at the front of the current group. "It wasn't _snarling_; it was _screaming_."

With that statement made, he turned his attention back to the pig, sitting silently beside it for the last few moments of its life before it finally passed away.

* * *

><p>A few moments later, with the soldiers having been ordered to return to their stations and wait for further instructions, the Doctor stood and stared at the body of the pig as it lay on a table in the morgue, now dressed in a yellow 'under-suit', Amy on one side of him and the doctor- who had introduced herself as Doctor Toshiko Sato- on the other, each of them contemplating the body in front of them.<p>

"I just assumed that's what aliens look like," Doctor Sato said, now calmer after her initial panic. "But you're saying it's an ordinary pig? From Earth?"

"More like a mermaid," the Doctor said.

"What?" Amy said, looking at him in confusion, her mind suddenly flashing back to the times a few kids at school had called her 'Ariel' after she started letting her hair grow out.

"Victorian showmen used to draw the crowds by taking the skull of a cat, gluing it to a fish, and calling it a mermaid," the Doctor clarified, his gaze still fixed on the creature lying before them. "Now someone's taken a pig, added… _thing_… to its brain, and turned it into a pilot for that ship."

"Oh god…" Amy said, looking at the animal in sympathy.

"Whatever part of it was capable of understanding this must have been terrified," the Doctor said grimly. "Whoever's behind this, they took this animal and turned it into a joke."

"Poor thing…" Amy whispered, looking sadly at the animal before them.

"So it's a fake," Doctor Sato said. "A pretend. Like the mermaid."

"Exactly," the Doctor said, revulsion obvious on his face as he stared at the table. "The original mermaid was sick, but at least everything was already dead; this pig was physically and neurologically mutilated while still alive…"

"But the technology augmenting its brain..." Doctor Sato continued, clearly uncertain about this news as she studied a clipboard in her hands. "It's like nothing on Earth. It's alien. Aliens are faking aliens. But why would they do that...?"

"I don't know," the Doctor said, his expression solemn as he looked back at her. "But I _will _find out."

With that solemn vow, he turned around and walked out of the morgue, Amy close behind him, leaving Doctor Sato staring between the door and the 'mutilated' pig as they briskly headed back to the main entrance.

"To the TARDIS?" Amy asked.

"To the TARDIS," the Doctor confirmed, his expression grim. "I have a couple of things I need to check up…"

* * *

><p>AN 4: There you have it; the first chapter of my new take on 'Aliens of London' and 'World War Three', which I hope will meet with your approval when it's all done (More obvious changes to the original version will appear in the next chapter, I assure you).<p> 


	24. Attack in Downing Street

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Hope this chapter meets with everyone's approval; I skipped over the scenes with Amy and Harriet Jones in the cabinet room as it was so similar to what originally happened to Rose that it wasn't worth rewriting, but those events will be discussed soon

The History of Paradox

"Right," the Doctor said a short while later, the two standing in the console room staring at a screen that displayed footage of the crashing ship, while a second screen that the Doctor had pulled up from underneath the console was remaining active as it searched for any fresh news broadcasts. "So, we know that the ship was real, but the pilot was fake; it must be a cover for something…"

"But a cover for what?" Amy asked, looking at her friend in confusion while trying not to fidget; her current attire looked smart, but it also wasn't entirely comfortable. "So far all they've done is put Earth on alert for something else to happen; isn't that a bit… counter-productive if you want to invade?"

"Good point," the Doctor said, nodding in confirmation as he stared grimly at the screen scanning the news bulletins, which were currently talking about an increasing sense of panic among the local population; apparently at least three people had been attacked on suspicion that they were aliens already, along with an increased amount of panic as the government failed to show any sign of taking action. "What now…?"

He stood in silence for a moment, contemplatively studying the controls in front of him, before he nodded and began adjusting levers and tapping controls, moving from one console to the other, until he smiled in relief. "Got it!"

"Got what?" Amy asked.

"Well, if someone's got a plan for Earth of some sort, they'd need to actually _be _here to put in action," the Doctor explained as he looked over at Amy with a smile. "With that in mind, I tapped into the planetary radar system- along with a few stations I set up myself back in the seventies-, looped it back twelve hours so we can follow the flight of the spaceship…"

He smiled as he looked at the screen, only for his smile to falter as he took in the data it was displaying. "Hold on; according to this, the spaceship did a slingshot _around_ the Earth before it landed…"

"What does that mean?" Amy asked curiously, as the Doctor thoughtfully studied the screen.

"It means it came from Earth in the first place," the Doctor said at last, looking thoughtfully at the screen as he considered this new information. "Whoever those aliens are, they haven't just arrived, they've been here for a while; their ship went up somewhere else and came down here."

"So… they've already arrived?" Amy asked, shivering slightly at the thought.

"Precisely," the Doctor said, looking grimly at the screen. "Now then, since you don't send something that big somewhere where you can't easily get to it on purpose, and there's been no sign of activity from that ship apart from the recovery of the pilot, we know they must be in this city already-"

"Do we?" Amy asked, looking inquisitively at the Doctor as he turned to look at her. "I mean, I know we haven't seen anyone leave the ship, but couldn't they have… transported out or something?"

"Teleportation systems, you mean?" the Doctor said, smiling in approval at her before his expression became more of a frown. "Good guess, but it doesn't work; teleportation is possible, of course, but I ran a quick scan of the local area and there's been no such signals sent anywhere since that ship crashed; since nobody would bother cloaking for that kind of energy on a planet like Earth, there's just nothing to cloak."

"Oh," Amy said, slightly dejected.

"It was a good guess, Pond, don't think it wasn't; it just wasn't right _now_, but that doesn't mean you won't be right to suggest something like that later," the Doctor said, smiling reassuringly at her before he continued. "The point is, if the aliens are here already, what have they been doing?"

He paused for a moment and shook his head. "Too many possibilities and not enough known about them as individuals to answer that right now; on the other hand, from _this _perspective, what do the professionals do when dealing with such an obvious invasion…?"

"What professionals?" Amy asked.

"_Your _professionals," the Doctor clarified, looking briefly at her before turning his attention back to the TARDIS, his hands quickly moving over the controls. "Right; a short hop to pick up Bessie, and then I need to move the old girl elsewhere…"

* * *

><p>As they walked up to the most famous door in the country, Amy didn't know if she should whoop for joy or scream in panic.<p>

She- Amelia Pond, the Scottish girl in the English village of Leadworth, the girl whose only friend aside from a centuries-old alien was a loner gay kid who hadn't even admitted what he was to anyone else yet- was walking into _10 Downing Street_?

She knew that the Doctor had some government connections- the stories he'd told her about his exile on Earth had been some of her favourites, even if part of that had been because she liked the fact that he'd _chosen _to stay on Earth for her this time around rather than getting stuck like he'd been back then-, but the idea that he was known about to the point that they wanted him to address _Downing Street_…

Even if she was only here because of her association with him, the fact remained that she had been invited to attend something that nobody else her age could even _imagine _getting to do; that was just…

_Wow_.

Even the moment when she and the Doctor were separated as he was shown towards a conference room further into the building and she was redirected somewhere else couldn't totally dampen Amy's enthusiasm; maybe she wasn't part of the main meeting, but she was still _inside_ Number 10.

She was just starting to wish that she actually had something to do other than stand around and look good in her near-suit-like-clothes while the Doctor headed off with the scientists; just because she didn't have official clearance, even after the Doctor had vouched for her, she had to stand back and wait while her friend went off to talk with the local experts.

She knew that it had to be done, and the Doctor had seemed very apologetic about it, but that didn't mean she didn't resent it being rubbed in that she was still 'in training'…

"Excuse me," a voice said, drawing Amy's attention away from her friend and towards the speaker, who turned out to be an older woman with shoulder-length hair in a white jacket and knee-length skirt. "Are you here with that… Doctor?"

"Yes," Amy said, looking uncertainly at the woman; she knew that the woman probably had some role to play if she was here in the first place, but that didn't mean she was going to trust anyone instantly when dealing with stakes as high as this situation might be. "And… you are?"

"Harriet Jones, MP for Flydale North," the woman said, briefly showing Amy her pass before lowering her voice. "The doctor you came here with… he knows about aliens?"

"What he doesn't know isn't worth knowing," Amy replied firmly, even as she lowered her voice to match the older woman's. "What's wrong?"

The woman seemed like she was about to reply, but instead she broke down in tears, leaving Amy to awkwardly give the older woman a hug while trying not to feel too panicked at this turn of events.

She might not be experienced enough to be allowed into the conference room with the Doctor, but she knew enough to know that anything that could make an older woman break down like this _had _to be bad…

"Uh…" she said, stuck for anything else to say in this situation that wouldn't sound stupid later. "What… what's wrong?"

* * *

><p>The Doctor might officially be the ultimate expert in alien affairs, but he wasn't going to dismiss any input that others might have to offer; he just found it frustrating that nobody he immediately recognised was in the room as well. He supposed it made sense, in a way- with the city on lockdown until they were sure of what was happening, there was no way to get the Brigadier or the rest of his old UNIT colleagues in, and that was even assuming any of them were in the country right now-, but talking to a group that consisted of people he'd only met a few times still wasn't his idea of a good way to tackle this situation…<p>

Besides, the booklet they'd been provided with as a summary of the situation was laughably basic; it had a few potentially interesting details about their observations on the ship and its crash-landing, but it was nothing that he hadn't already deduced from his own observations and analysis, so he was just going to focus on the immediate facts.

"Ladies and gentlemen, I'd like to have your attention please," General Asquith said as he stood at the front of the group, along with the current emergency Prime Minister, Joseph Green. "As you can see from the summaries in front of you, the ship had one porcine occupant-"

"Yes, that's all interesting, but what's _really _important happened three days ago," the Doctor said, standing up and walking into the middle of the room; as always, as far as he was concerned, respect for rank and/or status was one of the things that had to be forgotten in the face of a threat like this. "You see, satellites detected an unusual radioactive blip around that time, but investigations were cut off when all this happened."

Diving into the explanation might be a bit rude, but the Doctor had more immediate priorities than politeness right now; if he was right, they were about to face a serious problem, and he didn't have time to be courteous to everyone else if it meant taking longer to fill them in on the facts.

"In other words," he said, looking firmly at the group gathered around him, "someone _wanted _your attention focused here rather than there; the question is who and why? If aliens fake an alien crash and an alien pilot, what do they get?"

His eyes widened in realisation.

There was definitely something else going on here- this was far too elaborate and public for it to be just about getting them in one place-, but that was the most immediate advantage.

"Us," he said grimly, the other experts looking at him in obvious intrigue at his theory. "They get us. It's not a diversion, it's a trap. This is all about us; alien experts, the only people with knowledge of how to fight them, gathered in one room…"

The sound of a fart prompted the Doctor to turn around and look at the acting prime minister, wrinkling his nose slightly at the smell.

"Look," he said, staring at the larger man, "I understand that you're under a lot of stress right now, but you really should see about getting that looked at…"

His voice trailed off as the PM and the general laughed mockingly at him before the general removed his hat and undid what appeared to be a zipper on his forehead, revealing a glowing blue light that was rapidly replaced by a large alien figure emerging from the man that was apparently merely some kind of skin-suit. The emerging creature didn't match anything that the Doctor had seen before, being a paleish green with long three-clawed arms and large black eyes as well as being very obviously overweight by most worlds' standards, but it was definitely not something he wanted to be facing right now with no means of defending himself when the enemy were clearly in control of the current environment (The roars it was making would normally have prompted him to run, but he still didn't know enough about what he was up against to risk provoking them…).

"We are the Slitheen," the alien said, its voice deep and slightly distorted, as though it was talking through a layer of mucus.

"Thank you all for wearing your ID cards," 'Joseph'- assuming it had ever been him; the man he was looking at could have been replaced or he could have been part of a complex infiltration plan from the first place- said, removing a small control device from his pocket "They'll help to identify the bodies."

With that statement, he pressed a button on top of the switch, and the Doctor suddenly fell to the ground as an electrical charge erupted from the ID card to envelop his body, the same crackle of electricity from around him all that the Doctor could register to confirm that the same thing was happening to everyone else in the room…

_NO_! he thought to himself, his mind made up as he recalled how he had managed to take the power of Mondas's engines in his fifth incarnation.

Electricity channelled in this manner was far from comfortable, but if he could withstand radiation poisoning for ten years before dying, he could deal with the current being generated this stupid thing, _especially _when he had to listen to that fat thing's sickening laugh to give him something else to focus on…

"Sorry," he said, as he forced the card-like device off his chest and held it out in front of him, enjoying the fake P.M.'s shocked stare, "but I'm not going down _that_ easily!"

With that statement, he hurled the device at the creature that had earlier been posing as General Asquith, subsequently turning around and running for the door as the card left the creature screaming as it struck its collar, his mind already racing through his available options.

He didn't have the time to try and save anyone else in that room- after taking that amount of electricity for that long, any human that wasn't dead soon would be-, he had to assume that the aliens could get those skinsuits back on before he could find anyone to help him, and without any of his personal contacts immediately available the soldiers would be more likely to side with the apparent officials rather than the stranger in the bow tie (It might be cool, but he was too young to have an effective 'command presence' in this body), which meant that his best bet now was to find Amy, get somewhere secure, and work out what they were dealing with before it was too late.

Pulling out his sonic screwdriver, the Doctor ran a quick scan for any residual artron energy in his immediate vicinity, quickly identifying Amy's location- the trips might have been brief, but she was still giving off more energy than anything else in this building right now-, leaving him with an easy target to aim for. Dashing towards the stairs as he heard footsteps coming from the other direction- whether they were more 'Slitheen' or just normal soldiers, he didn't have the resources or time to deal with or convince either respectively-, the Doctor ran upwards, the sonic screwdriver out in front of him, focused on tracking Amy's location. Pausing only to grab a fire extinguisher as a potential weapon, the Doctor hurried along until the screwdriver had directed him to a state room with another Slitheen standing in it; Amy was probably hidden behind one of the chairs or curtains.

"What-?" the Slitheen began as it turned to look at him (The tone of voice suggested female, but the Doctor had encountered a few species that didn't consider gender a factor and he wasn't going to start making assumptions just yet), before the Doctor aimed the extinguisher and fired it at the Slitheen.

"_Amy_!" he yelled as the green thing staggered back, clearly off-balance from the burst of CO2 that had just hit it. "Get out of here!"

Even as he spoke, Amy was running out from behind a curtain as an older woman in a white suit leapt up from behind a chair, Amy grabbing the curtain to throw it over the disorientated Slitheen before the two women joined him at the door.

"You are?" the Doctor asked, glancing at the woman.

"Harriet Jones, MP for Flydale North," the woman replied automatically.

"Nice to meet you," the Doctor said briefly.

"Likewise," Harriet replied, looking back at where the Slitheen was removing the curtain from over her head. Stuck for other options, the Doctor threw the extinguisher at the Slitheen, striking it in its fat stomach before grabbing Amy and Harriet by the arms and running out of the room.

"We need to get to the cabinet rooms!" the Doctor yelled, ignoring the sound of roars from another corridor; if the other Slitheen from downstairs were up here already, all he needed right now was for them to keep roaring so that he could go the other way until he found somewhere better to hole up.

"The emergency protocols are in there," Harriet said as they ran. "They've got instructions on aliens!"

"Couldn't hurt," the Doctor said, quickly leading the way to the cabinet room- one advantage of Downing Street was that the interior never really changed; he'd come here for a few meetings when he was exiled to Earth and that memory was all he needed to retrace his steps-, the sound of something practically rampaging after him enough to confirm that the Slitheen were still in pursuit. As he entered the cabinet room through a side-door, the Doctor left Amy to look the door as he headed for another door. As he took in the sight of a Slitheen standing there, he spun around, screwdriver in hand, and grabbed a bottle of brandy from a nearby table, holding the screwdriver up against it as he glared at the approaching Slitheen.

"One more step and I'll triplicate the flammability of this alcohol; stay back and we all stay unburned," he said, his tone rushed to hopefully conceal the fact that he was completely stuck for what to do right now, staring at the Slitheen for a moment before they stepped back. "Right then, time to start talking; who are the Slitheen?"

"They're aliens," Harriet said from behind him, the Doctor biting back the brief thought of saying that he was already aware of that; it wouldn't help anything right now.

"Who are you, if not human?" the Slitheen said, in a voice that sounded slightly like that of the fake prime minister; they must have ordered the humans to remain downstairs if they were being that casual about their true appearances right now.

"Who's not human?" Harriet asked.

"He's not human," Amy said briefly.

"He's not human?" Harriet said, looking at the Doctor in shock.

"Let's just focus on the _immediate_ situation right now, please?" the Doctor said, briefly looking back at Harriet before turning his attention back to the Slitheen. "I'll ask again, what are you doing here? Invasion?"

"Why would we invade this God forsaken rock?" the Slitheen that was disguising itself as Joseph Asquith said in a condescending tone.

"Then why _are _you here?" the Doctor asked. "What do the Slitheen want with Earth?"

"Family business," the Slitheen said.

"Family business?" the Doctor repeated, lowering the screwdriver slightly in surprise.

"Slitheen is not our species, Slitheen is our _surname_," the alien clarified. "Jocrassa Fel Fotch Pasameer Day Slitheen at your service."

"OK, so you're a family, which means you wouldn't have the resources to conquer anything- weight of numbers can overpower any technology, as anyone knows; look at Applegate, after all-, so what _are _you doing here?" the Doctor asked, still staring intently at the Slitheen. "If you want to make a profit for your business, what can this 'god-forsaken rock' have to offer you?"

"Ah… excuse me?" another Slitheen said, sounding like the Slitheen that had been posing as the general downstairs. "Your device will do what? Triplicate the flammability…?"

"Oh, you noticed that was a load of rubbish?" the Doctor said, shrugging as he stepped back slightly, tossing the brandy to Harriet; he'd managed to bluff them long enough to learn a crucial detail, and that was what mattered. "You'd better take that, Harriet; you might need it later."

"And now, we hunt…" the general Slitheen said, flexing his claws menacingly as he looked at the Doctor.

"Actually, it's not going to be that simple," the Doctor said with a casual smile. "If nothing else, I think you'll find _this _hard to get through."

Before anyone could ask him what he meant by that, the Doctor stepped back and pressed a switch near the door, causing a series of metal shutters to slide down over the door and the windows, leaving the Doctor, Amy and Harriet inside the cabinet room and the Slitheen on the outside.

"Installed in 1991," the Doctor explained with a grin as he turned to look at the two women. "Three inches of steel lining every single wall. They'll never get in."

"And… how do we get out?" Amy asked, looking uncertainly at the Time Lord.

"Ah," the Doctor said, looking at their surroundings for a moment before he smiled, reached into his inner jacket pocket, and pulled out a large black laptop. "Well, we'll worry about that later; on the bright side, we _do _have this."

"What?" Harriet said, looking at him in surprise. "How did-?"

"The pockets are bigger on the inside," the Doctor said with a smile, as he patted his jacket before he looked at the computer in his hands. "Of course, I need to do a bit of work with this- I just grabbed it in case; I've not actually _needed _it yet, so it's fairly basic-, so, while I'm working on this, could you two fill me in on what you've found out so far?"


	25. Averting World War Three

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

The History of Paradox

As he sat at the table of the cabinet room, tapping away at his new laptop, the Doctor considered what he'd just heard from Amy and Harriet Jones.

After he'd left her while going off to his meeting with the other alien experts, Amy had been approached by Harriet Jones, who'd been looking for help after she'd witnessed the Slitheen claiming a new skin-suit, who had told Amy everything she'd seen and heard. Their attempts to search the cabinet room for more information about the aliens had resulted in the discovery of the Prime Minister's body in a cupboard before they were discovered by the third female Slitheen he'd seen earlier. She'd killed another Downing Street official who'd discovered them- Harriet had apologetically noted that she didn't even know the man's name-, but his attack on the other Slitheen downstairs had apparently had enough of an effect on the one up here to give the two women time to escape to the room where he'd discovered them, and he knew the story from there.

It wasn't much, but it was enough for him to be sure that he wasn't dealing with an impulsive attack; whoever the Slitheen were and what they were on Earth for, they had clearly taken great care to be ready for whatever they were trying now.

"OK," Amy said, looking between the other two as the Doctor sat at the desk working on the laptop and Harriet stood off to the side, "I get that these Slitheen things have infiltrated the government, but I _don't _get why they had to kill the Prime Minister; wouldn't it have made more sense to take his place?"

"They would have if they could," the Doctor replied with a shrug. "Unfortunately, their mass conversion technology appears to be comparatively limited; as we saw, they can compress themselves down to a degree, but the compression field's still limited."

"And the… smell?" Harriet asked.

"Result of the surplus gas exchange; all natural, if a bit smelly," the Doctor said, before focusing his attention back on the computer; he was still partly trying to place where he'd heard the name 'Harriet Jones' before now, but this wasn't the time to wonder about that. "Anyway, what about those emergency protocols you told us about? Is there anything useful there?"

"All redundant, I'm afraid," Harriet replied, indicating the folder in frustration. "They list the people who can help, but everyone who could be reached is dead downstairs."

"And there's no point trying to get something bigger that we could throw at them because the ship they have that we know about is out there, and we can't blow that up without possibly blowing _us _up," Amy added grimly.

"Besides," Harriet added, "nuclear strikes need a release code, and that's kept by the United Nations."

"Improvement over the days when things were so unstable they needed to give those codes to a neutral country…" the Doctor said, his tone reflective as he looked back at those old days, before he looked sharply at Harriet. "Are you saying that the government can't launch a nuclear attack without permission from the U.N.?"

"Exactly," Harriet said, nodding grimly at him before looking more curiously at the Doctor. "Is that important?"

"It could be," the Doctor said thoughtfully, still working at the computer. "Of course, we're not going to get anywhere if we don't know what the Slitheen are here for in the first place; considering that we're dealing with a family business, there must be some kind of asset they need here…"

"Like what?" Harriet asked. "Gold? Oil? Water?"

"Good guesses, but no; there are other planets with those assets that they could reach with their technology that would mean they wouldn't have to worry about impersonating local officials," the Doctor said, looking apologetically at her before he turned his attention back to the computer. "No, there has to be a reason for them to come here; the only question is _what_…"

"Couldn't we phone for help?" Amy asked. "You must have contacts…"

"Anyone who wasn't downstairs is too far away to help us out directly, and even if I could reach them, they can't get anyone to take action without evidence that they can't provide," the Doctor said grimly, before another thought came to him. "And on that topic, why did they make it so public?"

"To get everyone together?" Amy asked.

"They could have staged something more low-key if they wanted to get the alien experts in one place; why would they need to make it this public?" the Doctor countered, even as he opened up a web page on the laptop and began to tap away as he entered a particular password. "The Slitheen were hiding and put the entire planet on alert; where's the point in that?"

"What are you doing?" Amy asked, looking at the Doctor as he clicked on a link on the site.

"We know that the Slitheen have a ship out there; I'm just checking a few likely frequencies to see if it's transmitting anything…" the Doctor began, looking thoughtfully at something on the screen. "It looks like some kind of message…"

"Saying what?" Amy asked.

"No idea; it's on a repeating loop, but I don't have translation software on this thing to work out what it's _saying_ in that loop," the Doctor explained, shaking his head in frustration as he studied the laptop, before he sat back and stared thoughtfully at the ceiling. "OK, let's see what we have to work with… judging by face, colour, shape, and other abilities, that narrows their planet of origin down to a certain amount of planets within travelling distance… compression technology and slipstream engine… how did they hunt?"

"They talked about it like it was a… ritual thing; does that help?" Amy asked.

"Possibly," the Doctor noted, nodding thoughtfully at Amy. "Anything else?"

"Well," Harriet said, looking thoughtfully at them, "did you notice, when they fart- if you'll pardon the word-, it doesn't just smell like a fart- if you'll pardon the word-; it's something else, what is it, it's more like, uh… um…?"

"Bad breath?" Amy asked, wrinkling her nose slightly at the memory of the scent in question.

"That's it!" Harriet said with a smile.

"Got it!" the Doctor said, grinning as he stood up from his seat. "All those things taken together give us _one _planet; Raxacoricofallapatorius!"

"Oh," Amy said, blinking in surprise at that news. "That's… uh…"

"Yes, it's a long name, but that _does _give us some ideas," the Doctor explained, grinning at her in satisfaction. "Firstly, on a physical level, it means that the Slitheen are vulnerable to exposure to vinegar- not much, considering our lack of access to a kitchen, but it's something-, and secondly, it reaffirms that they aren't an invasion force; Raxacoricofallapatorius has a very stringent justice system, and a criminal family as organised as the Slitheen means that they could only be here if they had been exiled from their world…"

"Exiled?" Amy and Harriet repeated curiously.

"Attacks on inhabited planets like this are a serious offence; you wouldn't do something like that unless you were already in trouble so a few more crimes wouldn't make much difference," the Doctor explained, his smile fading to become a grim stare as he contemplated that discovery. "The only question now is what they're going to _do _here…"

"Hey," Amy said, looking out of the window at a group gathered in front of the building, "would a press conference taking place outside Downing Street be a good opportunity to get some answers?"

Hurrying over to the window, the Doctor immediately saw what she was looking at, a large press conference with various cameras and microphones all set up in front of the door, before turning back to the laptop.

"What are you doing?" Amy asked, looking at him curiously.

"It's a long shot, but I _think _I can tap the broadcast frequencies of those cameras and intercept the signal they're sending…" the Doctor said, his mind focused on his goal as his fingers raced over the keyboard; he was basically trying to write the code for BBC iPlayer over two years before it would actually go live, but as long as he deleted it afterwards, it should be al right…

"…_the news I bring you now is grave indeed_," Joseph's voice said as the Doctor finally finished his work; the laptop didn't have the memory capacity to display a live image, but he was able to stream the audio from the cameras, particularly when it was happening right outside the building they were currently in. "_The experts are dead. Murdered, right in front of me by alien hands. Peoples of the Earth, heed my words. These visitors do not come in peace__. __Our inspectors have searched the sky above our heads and they have found massive weapons of destruction, capable of being deployed within forty-five seconds__. __Our technicians can… baffle… the alien probes, but not for long. We are facing extinction, unless we strike first. The United Kingdom stands directly beneath the belly of the mother ship. I beg the United Nations- pass an emergency resolution. Give us the access codes! A nuclear strike at the heart of the ship is our only chance of survival. Because… from this moment on… it is my solemn duty to inform you… planet Earth is at war_."

"He… _is _lying about that, right?" Amy asked, looking anxiously at the Doctor.

"He's lying about the alien fleet stationed above us, all right- I would have detected something like that in the TARDIS earlier-, but the question is why he's exaggerating the scale of the threat," the Doctor said grimly. "What do they have to gain by accessing the nuclear defence codes…?"

He clicked his fingers in inspiration before he turned around and walked up to the door of the cabinet room once again, opening it to glare at the Slitheen standing on the other side.

"That's what this was all about, isn't it?" he said, staring scathingly at the Slitheen posing as Margaret Blaine as she stood in front of another three, taking care to position himself so that nobody could see his laptop on the table; so long as they thought he was still trapped and completely cut off from the outside world, he still had a chance. "Get the nuclear launch codes, fire the missiles at the other countries, and then… let me guess, hide out in your spaceship while the human race blows itself up?"

"Precisely," Margaret said, grinning in satisfaction at his deduction. "It's not crashed; just parked, within two minutes' walk."

"But you'll destroy the planet, this beautiful place," Harriet protested, looking at Margaret incredulously. "What _for_?"

"Profit," the Doctor said, the final pieces falling into place, his eyes narrowing as he looked at Margaret. "That's what your ship's doing out there; it's sending an advert into space, right?"

"Sale of the century," Margaret confirmed, still grinning in malevolent satisfaction. "We reduce the Earth to molten slag, then sell it, piece by piece. Radioactive chucks capable of powering every cut-price star liner and budget cargo ship. There's a recession out there, Doctor. People are buying cheap. This rock becomes raw fuel."

"By blowing up over six billion people?" Amy said, looking at Margaret in horror.

"Bargain," Margaret said dismissively.

"Right," the Doctor said, looking firmly at the woman before him. "Margaret Blaine, or whatever you call yourself, sine you haven't actually fired those missiles yet, I give you this one chance; leave Earth, _now_, or I _will _stop you."

The laughter that greeted the Doctor's statement was all the confirmation he needed that they weren't going to go along with his request, but he had felt obligated to make it.

He might have tried harder to talk them down in the past, but with a threat on this scale and no Time Lords to mitigate the worst of the historical damage- to say nothing of the ever-present issue of the Faction-, he was going to have to resort to more immediate measures.

"Right," he said, closing the door once more before turning around and walking back to the main table, sitting down in front of the laptop and pulling up the UNIT website once again. "We've got some time before the UN agrees to release the codes, but best to get this done sooner rather than later; if I can hack the Royal Navy via the UNIT site, I can issue an order to launch a missile at Downing Street and taking the Slitheen out of the picture…"

"Uh… you're going to shoot a missile at Ten Downing Street?" Amy said, looking uncertainly at the Doctor. "As in, you're going to shoot a missile at the building we're _in_?"

"We're in the most secure room in the building and we're facing the imminent destruction of the planet if we don't do something fast," the Doctor said, looking grimly up at her. "This is what I do, Amy, every time, every day, every second… I make the decision that nobody else can or will make, because the alternatives are almost always worse."

Looking at him now, Amy could suddenly _feel _the weight that her mysterious friend had carried with him for so long.

Whatever he'd had to do in the past, whatever he had faced before travelling with her… there were always going to be some things that he would regret doing.

"Do it," Harriet Jones said, looking firmly at the Time Lord.

"Excuse me?" the Doctor said, looking back at her.

"As the only elected representative in this room chosen by the people for the people, on behalf of the people, I command you; do it," Harriet said, her tone resolute despite her earlier doubts.

"Right," the Doctor said, smiling briefly at her before turning back to the laptop and the displayed web site. "We don't know how long we have, so better safe than sorry; right now the Slitheen are going to be contained up here, and they're going to prefer to be in their natural state at the moment of victory, so if we act now we make it harder for them to get away later…"

After a few moments of rapid tapping at the keyboard, he stood up and looked at the two women with a grim smile. "It's done; missile is on its way."

"Now what?" Amy asked, indicating the door to the cupboard where they'd found the Prime Minister earlier. "Stand in the doorway and ride this out like an earthquake?"

"Nothing better to try right now, so yes," the Doctor said, indicating the door as he picked up the laptop, staring urgently at the screen as he moved. "Just need to keep this on the go, make sure nobody intercepts it…"

As he followed Amy and Harriet into the cupboard, the Doctor could only keep his fingers crossed on the hand holding the laptop as the other hand hovered over the keyboard, ready to take action as soon as it was required; he could hold his own against most computer programmers if he had full access to peak resources, but there was only so much he could do with only a laptop to work with.

As an alarm blared around them, warning the rest of the building to evacuate, the Doctor could only hope that what he was attempting would pay off; this might be the only way to stop a larger war, but he didn't want to sacrifice anyone else if there was a chance that they could get out…

"Nice meeting you both," Harriet said, smiling at them as they crouched down in the cupboard underneath a shelf, holding hands and waiting for what was about to happen.

They were doing everything they could to survive, but, as he looked at the two people sitting around him, the Doctor found that the thing he was most concerned about was Amy; saving the world might be his priority, but he still wished that he'd had more time to show her some of the wonders of the universe. He was planning to start travelling with her full-time next year; why did this have to happen _now_…?

The sound of what could only be the missile striking Downing Street filled the room, shaking the building and sending the cupboard rolling as the cabinet room fell from its original position onto the ground below.

"Did… is it over?" Amy asked, looking anxiously at the Doctor.

"Just a moment…" the Doctor said, leaning over to press one ear against the wall, before stepping back and nodding at her in confirmation. "It's over; all quiet out there."

With that said, he quickly moved over to the small door opposite their temporary shelter and kicked out at it, smiling in satisfaction as it fell away to reveal a rubble-strewn street.

"Made in Britain," Harriet said, looking around herself with a smile as she patted the metal room they'd just been using as a shelter; it might not have been designed for that kind of punishment, but the designers had definitely outdone themselves nevertheless.

"Are you all right?" a military man, hurrying over to them with a clear expression of shock on his face.

"Harriet Jones, MP for Flydale North," Harriet said, showing the other man her ID card. "I want you to contact UN immediately, tell the ambassadors the crisis is over and they can step down. Go on, tell the news!"

"Yes, ma'am," the sergeant said, hurrying away with a bemused expression on his face at the abrupt turn of events.

"Someone's got a hell of a job sorting this lot out," Harriet said, indicating the rubble around her with a frustrated wave of her hand. "Oh, Lord! We haven't even got a Prime Minister!"

"Well, maybe you should have a go," the Doctor said, smiling warmly at her.

"Me?" Harriet said, looking at him in surprise. "I'm only a back-bencher…"

"Hey," Amy said, grinning over at her. "If I was old enough, _I'd _vote for you."

"Don't be silly," Harriet said, shaking her head before turning to look at the military and police representatives gathered at the end of the street. "Look, I'd better go and see if I can help."

As she climbed over the rubble, heading for the gathered crowd of cameras and ambulances, calling out for attention, the Doctor smiled as he finally placed the nagging sense of familiarity he'd felt when he first heard Harriet's name.

Give her a little time to get a good handle on what she was going to do with her time in office, and Harriet Jones would make a _very _positive impression on society in the not-too-distant future…

"So… what now?" Amy asked, looking up at him.

"Back to the TARDIS," the Doctor said, indicating another direction; thoughts of the country's future could wait. "There's a couple of back streets that way; we should be able to reach the old girl without anyone seeing us…"

"That's it?" Amy said, looking at the Doctor in surprise. "We just saved the world… and we're just _leaving_?"

"Do you really want your aunt asking what you're doing in London when you were meant to be staying in Leadworth?" the Doctor pointed out, smiling slightly at her before he shrugged, his expression becoming more grim as he spoke. "Besides, considering who we have to worry about, some secrecy is… probably for the best."

"What about the Slitheen ship?" Amy asked, as the Doctor turned and began to walk away from the shattered remains of Downing Street, Amy hurrying after him.

"Oh, I have a couple of favours I can call in to deal with that once we're back at the ship," the Doctor clarified, smiling reassuringly at her. "It'll take a little while, but it should be safe enough; they'll put that ship somewhere safe, and everything will be fine from there."

All in all, the Doctor had to admit that things had gone rather well. The last few moments had been a close call, but they'd managed to save the world and guide a prominent historical figure on the path to her destiny; if that wasn't a poke in the eye for Faction Paradox, he didn't know what was.

Plus, on a personal note, he was definitely proud of Amy's courage; he might want to keep her safe, but it was always good to see evidence that his companions could handle themselves when things were particularly bleak…

* * *

><p>AN: If anyone's wondering, Margaret Blaine didn't survive in this version of events; the Doctor launched the missile sooner than Mickey did in canon, and he was able to program it on a more direct route, so there wasn't enough time for her to escape, particularly since she was in her skinsuit and hence had no DIRECT access to her teleportation system.<p>

Once again, if anyone has anything they want to see, let me know; we've only got a couple of 'rewrites' left before this story ends and the Doctor and Amy begin their travels…


	26. Uncomfortable Revelations

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: Not the longest chapter, but it does cover an important emotional revelation for one of our protagonists…

The History of Paradox

It had been over a month since the confrontation with the Slitheen, and even now that she was back at school and the Doctor busy making sure that UNIT didn't do anything stupid with the salvaged Slitheen equipment, Amy still couldn't believe that it had actually happened.

She'd helped the Doctor deal with some interesting situations in the past, but their previous encounters with aliens on Earth had been focused around Leadworth or that military base where they'd encountered Sarah Jane Smith and her friends; even if she acknowledged that Prisoner Zero and the Shansheeth had a larger plan, it had never really reached the point where she could _see _what they would have done if they'd succeeded. This time around, however, the aliens had not only actually infiltrated the British government, but had come _this _close to acquiring the means to trigger a nuclear holocaust if they hadn't been blown up first…

It was slightly unfair that she and the Doctor didn't get any of the credit, but she understood why the Doctor didn't want it; not only would it risk attracting the attention of the Faction, but he didn't want to make his existence public and encourage people to depend on him (He'd told her all about the time some twisted Nazi scientist had stolen the TARDIS and used it to change history so that the Nazis won the Second World War; she'd spent virtually all her time going back and forth to ensure that the timeline she'd created remained intact, with the result that the new world she'd created almost literally couldn't cope without her).

Besides, their actions this time around had already done enough to set history on its prorper course. The subsequent emergency election had resulted in a landslide victory for Harriet Jones, and the Slitheen's ship had been claimed by the Doctor's assorted UNIT contacts, the Doctor assuring Amy that it was in a safe place after he had shut down the advert signal that they had been broadcasting. Analysis of the rubble had only revealed a few parts of the various Slitheen that they'd seen entering the building, but it was enough to confirm that the Slitheen had all been eliminated, each body-part featuring a different DNA pattern; the Doctor had actually stepped in to help identify them, and tests had confirmed that six Slitheen had been killed in the destruction of Downing Street, which were all that had been accounted for in those last moments before the building exploded.

It was actually funny, when Amy thought about it; looking back on the whole crisis, what disturbed and amazed her the most about her confrontation with the Slitheen was the fact that, when she'd come so close to being killed by the Doctor's own plan to stop the Slitheen and save the world… she'd _coped _with it.

She might not have wanted to die, but when it came down to a choice between staying alive for a few more minutes and taking a risk that would result in them saving the world, she'd made her choice, and she'd had the courage to stick with that choice no matter how scared she'd been.

If it was a choice between her life or the world, thanks to the example that the Doctor had given her- even if he wouldn't acknowledge that was the reason himself-, she'd had the courage to choose the world.

She knew on some level that the knowledge she was willing to die for something wasn't the kind of thing someone should have to learn at her age, but the fact remained that she'd been tested and she'd still managed to prove herself; that discovery had to be commendable even if the circumstances were scary.

What she was going to do with the Doctor might be dangerous, but it _mattered_; he had stayed around to ensure that she had every possible chance when she started travelling with him, and she wasn't going to waste that because she was afraid, particularly when she'd managed to confirm that she could cope with it.

Besides, what other sixteen-year-old could say that she had not only met the Prime Minister, but ensured her election to the post while saving the world from an alien invasion?

Opportunities like that were just one of the things she loved about-

_No_!

Amy didn't know where _that _thought had come from, but she knew she couldn't finish it; that could _never _happen! She _couldn't _think of the Doctor that way; he'd met her when she was _seven_, he'd never be able to- he was an alien- he'd been her teacher for the last few- he was so much older than- it'd be weird!

"Yeah…" Amy said, nodding reassuringly to herself, vocalising her thoughts to ensure that she understood her own point. "It'd be weird… yeah, it'd be weird… it's just a phase… he doesn't _see _me that way and it's just a little thing…"

The problem was, even if Amy could easily remind herself of the reasons why the Doctor wouldn't see _her _that way, it didn't stop her thinking of _him _that way.

He might look like he was at least a decade older than her and be chronologically much older than that- she wasn't sure of the exact age, even if she knew that his lifetime could be counted in triple figures at least-, but he never acted like he was that much older than her, which meant that it was almost easy for her to think of her as someone she could relate to on… on that level. He'd been the first person aside from Rory to treat her like she wasn't crazy once she started talking about her 'Raggedy Doctor', with the advantages of the Doctor being courageous, highly intelligent, and straight (The Doctor had mentioned a suggestive encounter with a French woman a few years back while Amy had never heard of Rory even going on a date; the evidence was good, anyway)…

God, now that she thought about it, she'd actually _resented _the woman in that story when she'd first heard it; was it possible that she really did… think of him that way…?

_No_.

She _couldn't_.

No matter how easy it was to forget the facts sometimes, she couldn't overlook the fact that he was a centuries-old alien who'd seen and encountered so many historical figures that she must appear slightly pathetic by comparison; he might have spent all this time teaching her about what she might encounter out there, but that didn't mean that she was anything more than a close friend… God, she was probably his _daughter_-

Amy stopped that thought instantly; the idea that the Doctor saw her that way might be a good guess, but that didn't mean it didn't hurt to think she might look like… _that_… to him…

It was just hormones, she told herself, sitting back down at her desk to continue her work; she'd been spending a lot of time with the Doctor over the last couple of years, he'd done a lot for her, it was only natural that she'd start… thinking about him like this… but that didn't mean there was anything _more _to it…

God, she was reminding herself of Rachel before she went to London after Phoebe's mistaken comment; she just _had_ to stop herself going any further before she… thought of something she couldn't cope with….

She was just grateful that the Doctor was off in London right now; at least she didn't have to worry about him sensing that something was off or something like that, and she'd have enough time to put everything in its proper place before everything went back to normal and he showed up again.

He was her friend, her teacher, and her guide to the wonders of time and space; that was more than anyone else could expect to have, and she would be content with that.

She had to be; she was too close to them officially starting to travel together to let it all fall apart because of a stupid little... _thing_…

* * *

><p>AN 2: Regarding future plans, I was originally thinking of re-doing 'Girl in the Fireplace', but decided that I didn't really see it working out- apart from anything else, Reinette worked with the Tenth Doctor's initial optimism about his new life before he lost Rose but might not connect as well with the Eleventh's subtle self-loathing, particularly when he's got his long-term guilt over the Faction to deal with-, so we're probably only going to have one more rewrite before the Doctor and Amy leave unless you have any modified Ninth or Tenth Doctor adventures you <em>really<em> want to see.


	27. The Christmas Invasion

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: The last episode rewrite for this story, as the Doctor and Amy face a very particular threat from canon in a very different manner to how it went originally…

The History of Paradox

"Christmas!" the Doctor said, grinning as he sat in the TARDIS wrapping Amy's present, grinning at the ship. "Always a good opportunity to celebrate, old girl; wouldn't you agree?"

The last few years had been fairly quiet by their standards- the Doctor couldn't recall the last time he'd stayed in one place this long when he didn't have to; his third incarnation had spent a fair amount of time on Earth even after his exile had been concluded, but that was partly out of an ingrained habit from his first few years rather than any specific interest in staying in one place-, but they were coming up to the end of Amy's training, along with the end of her time at school, which meant that they were almost ready to start their journey.

The only question now was what he was going to do for Amy when Christmas came around. As the last present he'd give her before they started their journey- her birthday was after she'd left school-, he wanted to make it something special, but the question was _what_…

Glancing at a screen in the console room showing the local television stations, the Doctor smiled as he saw Harriet Jones talking about a recent probe sent into space; she had only been elected recently, but the country was still doing rather well, particularly with Harriet's talks about the probe representing the country's ambition for the future and the probe's symbolism of the birth of a new age.

He was never sure why Britain as a whole had always attracted his attention more than the rest of Earth; maybe it was simply that he and Susan had chosen London as their original 'home' on Earth, or maybe it was considering the impact that relatively small island had made on the rest of the world, but this country would always remain one of his favourites, even if he hadn't made so many friends in his visits…

Shaking that thought off, the Doctor turned his attention back to the matter of Amy's present; something practical and/or comfortable were his top possibilities for consideration right now…

* * *

><p>As she sat in her aunt's house, staring idly at the TV out of a lack of anything else to do- her aunt was out doing some last-minute Christmas shopping and the Doctor had some things he wanted to work on in the TARDIS in private-, Amy once again found herself wishing that she could just start travelling with the Doctor; one of the best things about travelling in time, in her (admittedly limited) experience, was the chance to skip over the boring parts of the year and get right to the good bits (With the exception of birthdays, anyway; it wasn't really a birthday if you weren't a year older mentally as well, and that was without the fact that she didn't know if travelling in the TARDIS affected her age).<p>

It wasn't that it wasn't good to see Harriet Jones 'fulfilling the Doctor's prophecy' about what she'd accomplish in her future, but when you had a time-traveller for a friend you just wanted to cut straight to the interesting bits; living the slow path was becoming boring for her after seeing the future, and she'd lived it for most of her life.

OK, so it was slightly embarrassing and frustrating that she found herself thinking… those kind of thoughts… about the Doctor because he was willing to put up with that stuff for her sake, but she _knew _that nothing could happen; it wasn't like she was fantasising her life away dreaming of something impossible…

"_Scientists in charge of Britain's mission to Mars have re-established contact with the Guinevere One space probe_," the reporter on the current channel said. "_They're expecting the first transmission from the planet's surface in the next few minutes_."

"_Yes, we are_," a man that Amy vaguely recognised as the scientist responsible for the probe's construction said; he sounded slightly flustered, the impression being reinforced by the fact that he'd taken off the jacket she'd seen him wearing during an earlier broadcast, but still seemed as though he was in control. "_We're-we're back on schedule. We've received the signal from Guinevere One. The Mars landing would seem to be an unqualified success_."

"_But is it true that you completely lost contact earlier tonight_?" an unfamiliar voice said from off-screen.

"_Yes, we had a bit of a scare_," the scientist said. "_Guinevere seemed to fall off the scope, but it, it was just a blip; only disappeared for a few seconds. She is fine now, absolutely fine. We're getting the first pictures transmitted live any minute now. I'd better get back to it; thanks_."

As static blurred across the screen and new images appeared in front of her, Amy didn't need her long experience with the Doctor to know that she was looking at something unexpected, the dialogue of the broadcasters now irrelevant; she might not recognise the aliens in question, but she was definitely looking at something non-human.

"_Cattle_," the alien said, in a strangely twisted voice that went well with the face that put her in mind of a red-eyed goat's skull. "_You now belong to the Sycorax. We will own you. We now possess your land, your minerals, your precious stones. You will surrender or they will die. The Sycorax are stronger, the Sycorax are mightier, and the Sycorax have_ krisek-tianc_; you cannot match us_."

Amy might not understand what that last word meant- she guessed it was one of those terms that just didn't translate well into English, much like some of the Doctor's stories about how key time-travel concepts didn't have the correct tenses for some of the trickier temporal mechanics he told her about-, but she had understood enough to know that this was definitely not the positive kind of first contact the Doctor wanted Earth to experience when the time came.

With that thought, Amy got up, grabbed her coat, and ran for the door, heading for the Doctor's house as quickly as she could. Fortunately, the streets of Leadworth were fairly empty at this point- she guessed that people were all busy either preparing for Christmas or watching the recent broadcast, even if the TARDIS was the only reason she could understand what they'd just said. With no reason to be concerned about people seeing her hurrying to her friend's house, Amy made it to her destination in no time, the Doctor opening the door practically after the first knock.

"Yes?" he said, smiling hopefully at her before he took in her shaken expression. "We have a problem, I take it?"

"Aliens called the Sycorax just sent Earth a message calling us cattle and claiming that we belonged to them; I'd call that a problem, wouldn't you?" Amy asked.

"Sycorax?" the Doctor said, raising an eyebrow in surprise before he adopted a resolute expression. "In that case, we'd better be off; with that space probe your government launched recently, there's no telling what they could do with the material available."

"What?" Amy said, looking at him in confusion even as she followed him into the TARDIS. "But… they've already mastered space travel; if they wanted to hack us-"

"It's not them getting access to your technology I'm worried about, it's what they could do biologically," the Doctor explained. "Probes like that Guinevere One often include plaques identifying the human race as a kind of… message to the stars; these can include maps and music- not normally a problem; anything advanced enough to translate those could normally find you on their own- but can also include samples of plants, water, or blood."

"And that's a particular problem here?" Amy asked.

"To say the least," the Doctor confirmed grimly. "The Sycorax are fairly advanced, but they have a degree of ties to the Faction that could be a point for concern, particularly with their use of blood control technology; with a sample of a certain blood type, blood control technology would allow them to issue basic commands to anyone on Earth with that specific blood type, which could allow them to blackmail the world into surrendering by making it look as though everyone with that blood type will be commanded to kill themselves."

"Oh God…" Amy said, looking at him in horror at the image his words created. "You mean…?"

"They couldn't _do _it, of course- blood control's basically just technologically-enhanced hypnosis, and you can't hypnotise someone into killing themselves-, but it could certainly be intimidating enough to be a concern," the Doctor said, tapping a few controls on the console as he pulled up an image on the scanner, nodding thoughtfully at the sight of Earth with something coming towards it. "Add in their available resources, and they could mount a powerful offensive assault if blood control is disabled; if we're going to stop this, we need to get up to the ship."

"Why?" Amy asked.

"Because I can only stop them there," the Doctor said, his gaze shifting from Amy to the telepathic circuits before he sighed in frustration. "Honestly, we have to work on this; why did they have to get all the talent…?"

"Pardon?" Amy asked, looking at him in confusion at the sudden change of topic.

"The only way to deal with the Sycorax without a great deal of needless bloodshed and/or fear on both sides is to invoke their Sanctified Rules of Combat and challenge their leader to a duel for the planet," the Doctor explained, flexing his fingers as his hands hovered over the telepathic circuits, mentally preparing himself for what he was about to do. "Unfortunately, I'm not much of a hand-to-hand expert this time around- I've got some tricks, but nothing I'd be comfortable relying on with stakes this high- so I'm going to have to get some help from an old face."

"An… an old face?" Amy said, looking at him in surprise and anticipation, his brief explanations of regeneration and the pictures she'd seen of his old faces running through her mind. "You mean… you're going to bring one of your past selves here?"

"Not physically; mentally," the Doctor explained, tapping the relevant circuits with a smile. "My past personas are all still in my subconscious mind, so they're theoretically accessible; what I need to do is draw out one with a particular knack for sword-fighting- probably teeth and curls; he had a certain flair that might prove useful- and let _him_ do it."

"Can that work?" Amy asked.

"I've done it before, and that was when I was trying to defuse a bomb that could have blown up half the planet if it had gone off; I can make it work now," the Doctor said, placing his hands over the telepathic circuits. "I've set the coordinates to the ship and we're on our way, so I'm going to initiate the switch now, but you'll have to stay quiet; even if I want to do this, my present persona's going to try and reassert myself over my old self and the TARDIS's overlays, so we have to ensure that Scarfman has no reason to be distracted from the task at hand."

"Sure," Amy said, nodding at her friend. "Uh… good luck."

"Thanks," the Doctor said. With that statement, he placed his hands on the telepathic circuits, closed his eyes and tipped his head back, his eyes flicking under his eyelids as though he was having a dream, before his eyes opened. "Ah, there we are."

To Amy's amazement, the Doctor's voice even sounded different, being significantly deeper and slower-paced than the tone she was used to hearing from her friend; even his expression seemed slightly different, his eyes being slightly wider than she was used to seeing.

"Doctor?" she said uncertainly.

"That's me," the Doctor said, grinning at her before the central console stopped moving, prompting him to shrug off his coat and walk towards the door. "Now then, let's deal with this little bit of business, shall we?"

With nothing else to say to that, Amy joined the Doctor as he left the ship, finding herself in a large stone structure that looked more like a cave than a spaceship interior, filled to the brim with a large number of Sycorax clad in red robes, what appeared to be bones hanging on necklaces around their necks, and holding long wooden staffs (Amy privately wondered if they were actually wood or just looked like this, but this definitely wasn't the time to wonder about things like that).

"Hello!" the Doctor said, waving politely at a figure standing in the middle of the room, a small collection of guards on either side of him. "You're the leader of this group, I believe?"

"You are not of this world," the Sycorax said, looking at the Doctor in a pointed manner, a rasping edge to his voice that disturbed Amy even before the alien removed his bone-like mask to reveal a face that gave the impression he'd been partially skinned around his jaw and eyes, with his skeleton apparently sticking out of his face; did they naturally look like that, or did they remove the flesh from their faces as part of some kind of ritual, given the Doctor's comment about their ties to the Faction…?

"No," the Doctor said, looking grimly at the leader, "but I'm very fond of it, and I would greatly appreciate it if you decided to turn around and leave this planet alone."

"And why should we do that?" the Sycroax asked, sounding slightly amused at the suggestion.

"Because," the Doctor said, his eyes narrowing as he walked up to one of the guards and grabbed a sword from the guard's belt before it could react, the Time Lord stepping back and giving it a practise swing as he faced the Sycorax leader, "I have come to challenge you for the planet under the Sanctified Rules of Combat."

"You stand as this world's champion?" the Sycorax leader asked, drawing his own sword as he looked at the Doctor.

"Precisely," the Doctor confirmed, nodding at him with a broad smile before his expression became more solemn as he and his foe raised their blades before they knelt on the ground, staring at each other.

"For the planet?" the Sycorax leader said grimly.

"For the planet," the Doctor replied firmly.

With the apparent formalities exchanged, the two men stood back up, assumed a combat stance, and began to duel, swords clashing as the fight commenced. The Sycorax leader was clearly experienced at using his weapon, unleashing powerful blows against the Doctor, while the Doctor's current approach relied on parrying his opponent's own assault and staying out of his way, responding to his foe's initial attempt to force his sword out of his hand by retreating out of harm's way.

As the Sycorax leader hacked away with powerful swings, the Doctor remained on the edge, occasionally deflecting the blows with his own sword but otherwise moving just out of reach as the alien attacked. After a few deflected blows, the Doctor moved on to a more offensive approach, rapidly slashing and thrusting his sword at his enemy, forcing the Sycorax leader increasingly further on the defensive to avoid being struck. At one point the two ended up virtually face-to-face, swords in the Doctor's left hand and the leader's right, but the Doctor quickly backed off as the Sycorax leader struck him in the chest with his elbow.

"DOCTOR-!" Amy yelled, moving forward to help him.

"Stay back, Sarah!" the Doctor yelled. "Interference will invalidate the challenge and give him the planet!"

Under other circumstances, Amy would have corrected him on the incorrect name, but as he turned his attention back to the fight, this clearly wasn't the time to worry about that. As the two aliens continued to exchange blows, the Doctor danced around the central chamber, parrying blows as the Sycorax leader became increasingly vocal in expressing his frustration, raising his sword to hack away at the Doctor, the Doctor retaliating with desperately-parried blows until the leader thrust forward, clearly attempting to impale the Doctor with his weapon. A quick step to the side and a downward thrust trapped the Sycorax's blade in the hilt of the Doctor's own sword, followed by a quick twist on the Doctor's part yanking the weapon out of the Sycorax leader's hands, followed by the Doctor ramming the hilt of his enemy's former weapon into the leader's chest to send him falling to the ground, the Doctor's sword at his throat before he could move away.

"I win," the Time Lord said, standing over the Sycorax leader with a grim stare.

"Then kill me," the Sycorax leader said, glaring at the Doctor.

"I'll spare your life if you accept this champion's command," the Doctor said, staring firmly at the leader. "Leave this planet, and never return. Is that understood?"

"Yes," the Sycorax said, glaring up at the Doctor.

"Swear on the blood of your species," the Doctor said, pressing the sword into the leader's neck.

"I swear!" the Sycorax leader practically spat at him.

"Good," the Doctor said, stepping back with a satisfied smile, before he turned to look at Amy with a reassuring smile. "You see, Romana, no need to worry; all under control."

"I'm Amy, Doctor," Amy said, looking uncertainly at him.

"Oh, of course; sorry," the Doctor said, lowering his head for a moment before he looked up again, grinning at her in a more familiar manner that made it clear the Doctor she knew was in control once again. "Well, I'm glad that's over with; that kind of thing _really _gives you a headache…"

"You're all right?" Amy asked, looking anxiously at her friend.

"Oh, I'm fine," the Doctor said, smiling reassuringly at her. "Bit of a headache, as I said, but that's only to be expected from something like this; bringing out an old personality like that shakes up the brain a bit, like sticking a temperamental horse in an unfamiliar stable- no, wait, it's not like that…"

As the leader charged towards him with a sudden roar, the Doctor swung around to slam the side of his sword into his adversary's face, sending the Sycorax falling to the ground, clutching at his cheek in pain, a fragment of bone from what would be his cheek if he was human having been removed.

"Don't do that again," the Doctor said, glaring at the Sycorax as it lay on the ground. "I'm trying not to be what I could be, but that _will _only earn you so much leeway. Is that clear?"

The leader hissed angrily at his opponent, but the way he reached up to his damaged cheekbone made it clear that he was willing to end this particular confrontation. Nodding in satisfaction, the Doctor turned around and walked back to the centre of the room, looking at the massive chamber with a solemn expression.

"By the ancient rites of combat," the Doctor said, as he stared at the vast numbers of Sycorax around the chamber, "I forbid you to scavenge here for the rest of time. And when go you back to the stars and tell others of this planet, when you tell them of its riches, its people, its potential…"

He paused for a moment as he looked around at the assembled masses, making sure all eyes were on him, before he finished his sentence. "When you talk of the Earth, then make sure that you tell them this; it. Is. _Defended_!"

With that proclamation, he turned around and walked back into the TARDIS, Amy following him with a broad grin as he shut the doors behind them and set the coordinates for Leadworth.

"Did you have to do that?" Amy asked, smiling at her friend as the TARDIS's familiar dematerialisation noise filled the room as the column began to move.

"The speech at the end?" the Doctor said, smiling at her in understanding. "Yes, I do; if I'm going to invoke the Sanctified Rules of Combat, I need to make the terms clear at the end, which meant the speech was necessary."

"OK," Amy said, smiling in understanding. "So… they're gone?"

"They're gone for good," the Doctor said solemnly. "We're not going to have to worry about the Sycorax for a while now, which means that we're going to get on with Christmas; shall we?"

* * *

><p>Later that night, as Amy sat on the sofa in the Doctor's living room, leaning against her Time Lord friend as the TARDIS stood silently in the corner, she wondered what it said about her that she felt so much more comfortable here than she did back in her aunt's.<p>

With the crisis of the Sycorax invasion having been resolved so quickly, their initial transmission had been passed off as a student hoax hacking the Guinevere One computers, leaving Doctor Llwellyn to claim that this lost probe would have to serve as a prototype for the second version that would improve the probe's software defences. With Sharon having left after her and Amy's own Christmas party to attend a party with some colleagues from work, Amy had seized the opportunity to hurry over to join the Doctor, the two sharing another quick meal on top of Sharon's own meal before settling down to watch a film on television.

It had been a relatively impulsive decision on her part- she could have easily just stayed at home and asked the Doctor to come to her place; it would make it easier to avoid being caught out by Sharon if she came back earlier, since the Doctor could more easily sneak out of the house than she could sneak back in- but she preferred being here more; it was nice to be in a position where she and the Doctor could just… _relax_…

Even if she knew that things could never go beyond what they had at the moment, Amy could still enjoy spending time with her Time Lord friend, wearing the black fur-lined leather jacket he had just given her for Christmas, thinking about the alien wonders they'd encounter when she was ready to travel with him full-time after she left school this summer...

He would never see her the way she was trying to deny she was now seeing him, but they were friends, and she was the Doctor's student; that was more than virtually everyone else got…

"Amy," the Doctor said as the movie came to an end, his tone unusually pensive and his expression solemn as Amy looked up at him, "we need to talk."

* * *

><p>AN 2: Coming up, the moment you've all been waiting for;the moment when the Doctor reveals <em>how <em>this world differs from the world we know in canon, and the role that the Faction play in these events...


	28. The History of Paradox

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: A brief segment here is taken from the Eighth Doctor novel "The Ancestor Cell", but I will provide a background summary to put it in context; hope you like the results as I explain what happened in the Doctor's past that made him so skittish about the topic of the Faction…

The History of Paradox

"Talk?" Amy said, looking anxiously at him. "About what?"

"About my connection to the Faction," the Doctor explained, his expression still grim. "If you're going to travel with me, there are… things… you have to know, and it's best that you know them now so that you have time to make alternative arrangements.

"What?" Amy said, her eyes widening in horror at the implication of the Doctor's words. "You mean you don't-?"

"Pond," the Doctor said, holding up a hand to halt her mid-sentence, "I would _love _to have your company in my travels, but, as I said, there are things I haven't told you yet that may… affect your decision."

"Like what?" Amy asked, looking anxiously at her friend.

For a moment, the Doctor simply sat in silence, staring between his friend and the room around him, as though taking in his last sights of the life he'd made for himself here before he ended it through his own actions, before he continued talking.

"You obviously know about Faction Paradox," he said, deciding to begin at the beginning; they'd never discussed this issue by silent consent, but it was time for that to change. "Can you tell me _what _you know about them, precisely?"

"Just that… they're _there_, really," Amy said, shrugging uncertainly as she looked at him in confusion. "I mean, they have a whole thing about death for some reason, they've been around for a long time, they talk about the past and future being irrelevant and how the present's the only thing that matters…"

"All true," the Doctor said, nodding at her before he continued. "They're time-travellers, as you've already guessed, but their time-travel methods rely more on voodoo-esque rituals than anything else; it's a complicated system involving perception and belief that only their initiates can fully understand."

"OK…" Amy said, nodding in uncertain understanding as she looked at the Doctor.

"I originally only became aware of them in my fourth life- they were a dirty little secret but fundamentally harmless; they were more of a cult who hung around and talked about death and manipulated the social outcast into killing their grandparents before they'd met," the Doctor explained. "Frustrating to the Time Lords, of course, particularly when they sold small-scale time-travel technology to other races, but not actually _dangerous_…"

He sighed at the memory. "Until that mess with Dust and Saudi Arabia."

"Dust in Saudi Arabia?" Amy repeated.

"Dust _and _Saudi Arabia; Dust was a human colony in the thirty-eighth century that basically marked where humanity just gave up trying to expand further," the Doctor clarified. "Anyway, at one point three lives ago, I was trapped in a cell in Saudi Arabia- some Israeli group thought that I was involved with some espionage thing they were investigating; I never established what it was all about- and I ended up trying to use the time to carry out various temporal equations in a prison cell to try and work out the best way to resolve some paradoxes hanging over my current companion, which is a long and complicated story I'll tell you later if you want to hear it. I'm not sure if it was a mistake in my calculations or something someone else did, but I somehow found myself creating a door to the TARDIS belonging to one of my past selves, resulting in me not only alerting him to the Faction's existence before he should have found out about them, but also diverting my younger self's TARDIS to a different location than it should have materialised at."

"You… he… went to Dust?" Amy asked, evidently uncertain what term was the most suitable.

"I sent my younger self to Dust," the Doctor confirmed. "As a result, I not only met someone I was never supposed to meet- another complicated story I'll explain later if you wish to hear it-, but the resulting confrontation with some of the Faction's agents resulted in my third body… dying before he should have done."

"Oh," Amy said, looking at him sympathetically. "That… that must have been-"

"That wasn't the worst of it," the Doctor said.

"It wasn't?" Amy said, looking at him in surprise. "They _killed _you-"

"And infected me," the Doctor continued; this was the part of the story he still hated to remember, regardless of how vague the memories were, but it was something he couldn't afford to forget in this dark new world.

"Infected you?" Amy repeated, looking anxiously at him. "With what?"

"A paradox biodata virus," the Doctor explained, his expression grim. "Essentially, the Faction ensure the loyalty of new recruits by infecting them with a virus that manipulates their perception of the universe around them so that they will be susceptible to the Faction's point of view. Normally the virus wouldn't have been strong enough to infect me, but it basically 'sneaked in' while my body was occupied with my regeneration; my immune system would protect me for my next few lives, but the virus's influence on me would become greater each time I regenerated, until, by my eighth life…"

He shook his head in frustration. "Well, by the time I was in a position to learn what had happened to me, the virus would already be rewriting me into a member of the Faction."

"_What_?" Amy said, looking at him in horror.

"Well, that's what _would _have happened," the Doctor said, looking over at Amy with a smile as he indicated the blue box in the corner of the room. "Fortunately, the old girl had other ideas."

"The TARDIS?" Amy said in surprise. "What did it do?"

"Took the infection into itself," the Doctor explained, smiling affectionately at his ship. "It took a lot of energy on the old girl's part, and she took a few knocks towards the end- held on even after she materialised in a dimensional rift that nearly tore her to pieces- but she took the infected timeline into herself and preserved some fragments of what should have happened to my third self, saving me from the infection while leaving enough traces for the Faction to think that it was working on me…"

He sighed grimly. "Of course, that's where it all went wrong."

"What?" Amy asked, looking at him in confusion. "But the TARDIS-"

"Was so focused on protecting me she didn't realise what she was doing to everything else," the Doctor elaborated. "It's a complicated story, but in a nutshell, her actions gave the Faction the chance to penetrate my homeworld's defences while they were occupied studying the Edifice that she'd become- her attempts to contain the virus warped her structure into a massive bone formation; I'm still not entirely clear how she did that-, allowing them to mount an assault on the planet with their leader…"

He sighed. "And the leader was me."

"_You_?" Amy said, looking at him in shock.

"The me who would result from the Faction virus's contamination of my timeline," the Doctor elaborated. "The TARDIS was keeping the infection away from my current timeline, but it was still present somewhere… and in the timeline where I was infected, I would go on to become Grandfather Paradox, the personification of the concept of Paradox as the man who killed his past, the god and creator of the Faction as they created themselves…"

He solemnly shook his head as he stared at his hands, the memory of that nightmarish confrontation in the Capitol as he stared at himself, leather armour and a missing arm reinforcing the image of the monster that he would become, his other self glaring at him with a twisted insanity that even the Master had never demonstrated at his worst…

"It came down to a confrontation between me and him in the Edifice that the TARDIS had become trying to save me," the Doctor continued; like ripping off a band-aid, the sooner he could get this done, the better. "The Grandfather was convinced that all he had to do was wait for me to become him, but, as the Edifice produced a targeting lever, reactivating a long-dormant weapons system, I knew that there was only one choice left. I was able to fight my way past him and remove one of the dimensional stabilisers, unbalancing the Edifice's own stability, but then he forced me away from the console…"

* * *

><p>"<em>Listen to me, Grandfather!" the Doctor said, his tone slow and grave as he addressed the one-armed psychopath standing between him and the Edifice console, the stabiliser cube brandished before him. "The Edifice is losing form. It's grown to this colossal size by mapping its external dimensions on to those of its interior. It's as big inside and out… but the dimensional interfaces are fatigued, wearing thin. Now I've removed this, it won't take so much to bring the whole thing tumbling down."<em>

"_The device is useless," the Grandfather said, indicating the curved brass handle of the weapon systems. "It can't focus fire now; it's just a relic of the ancient times of conflict."_

"_You've helped bring those times upon us again," the Doctor said. "No one knows that better than the core of this poor, tired old TARDIS of mine."_

_As the Edifice pitched again, its floor becoming a steep gradient, the Grandfather stumbled over, his single arm adequate to support him as he fell, allowing the Doctor to stumble towards the console. The Grandfather grabbed him by the leg, but the Doctor managed to remove another stabiliser cube before he was pulled to the floor._

"_Let me go," he yelled, kicking desperately at the Grandfather as his other self scrambled up his body. "You wanted the power of the Edifice, you're going to get it."_

_"You're bluffing."_

"_No."_

_As the Grandfather smashed his head against the Doctor's own, the Doctor's senses were __sent reeling, but he was still able to force himself to focus long enough to launch one last punch at the Grandfather's cheek. As the Grandfather fell backwards, the Doctor staggered back to his feet, reaching for the console once more._

"_Just one bolt fired will drain off all the energy holding the Edifice together," he yelled. "The internal dimensions will collapse down to something the size of this stabiliser."_

_The Grandfather stared back at him. "Gallifrey, Kasterbourus… This entire sector of space will be destroyed, torn apart."_

_The Doctor nodded, eyes welling with tears. "Forever," he said firmly. "But your entire fleet will perish too."_

"_You'll die too."_

"_Just as well, I think," the Doctor said, gritting his teeth. "I'd never be able to live with the memory anyway."_

"_You will destroy all Gallifrey- wipe out millions of lives."_

"_I never thought I'd admit to choosing the lesser of two evils."_

_That proclamation made, the Doctor seized the device on the console, but the Grandfather __once again flew over to grapple with him, the Edifice's current angle preventing the Doctor from staggering out of the Grandfather's grip, his twisted reflection forcing the Doctor's right arm behind his back._

"_Give in to me," the Grandfather hissed contemptuously at him. "You know you can't bring yourself to do this."_

"_I must!" the Doctor gasped. "I will be sparing my people a war that will dehumanise them to the point of becoming monsters. I will be saving them from whatever living nightmares the Faction's technology can inflict upon them._

"_And yourself?" the Grandfather asked angrily._

"_I don't know which way this TARDIS will jump," the Doctor whispered. "Nor which timeline will be set in stone. But at least that's what it will be. Stone, not bone."_

"_I will ensure that the Faction's timeline is chosen," the Grandfather hissed in his ear. "You will never destroy the Faction. All of space and time is riddled with us."_

_As the Edifice tilted once more, both men tumbled away from the console, the Doctor's arm still pinned as he suddenly went limp in the Grandfather's grasp._

"_Riddled?" the younger Time Lord said, shaking from the grief of what he was about to do. "I'll give you a riddle. I've been thinking of a paradox- an extra-special one, just for you. That missing arm of yours, the stuff of your legend."_

"_I removed it myself," the Grandfather said, scowling at him. "To defy the Time Lords branding me their prisoner."_

"_No you didn't," the Doctor said, glaring contemptuously back at his future self._

_This man was his target, and he _would _be eliminated…_

"_You cut off your own arm because you used it…" the Doctor said as he gripped the lever with his free hand, the Grandfather's single arm occupied with holding down his other one, "…to do…" twisting down with all his strength on the lever as he screamed out the final word, "…this."_

_As he slammed his hand down on the control, the Grandfather smiled._

_"Thank you," he said._

"_What?" the Doctor said, looking at his possible future self in ever-growing horror._

"_You were correct," the Grandfather said, smirking mockingly at him. "I _did _cut off that arm because I destroyed Gallifrey… and you just gave us exactly what we needed to achieve true mastery of time."_

"_NO!" the Doctor yelled, lunging towards the Grandfather as he vanished in the familiar glow of a transmit beam, leaving him to stare in horror at the image being displayed on the Edifice's battered scanners. Precision focus was impossible with the amount of power the ship had lost, but he could still get a general picture of the surrounding area, and that was enough for him to stare in horror at the sight of the Faction's ships moving away from the blast radius._

_The blast of energy he'd just released from the Edifice's ancient weapons was heading straight for the heart of Kasterborous, packing enough power to annihilate Gallifrey, but the Faction's entire fleet was _moving out of harm's way…

_The Grandfather had tricked him._

_The Doctor had realised the significance of his lost arm as the Grandfather wanting to forget what he'd done, but he'd assumed that he could still take out the Faction's fleet if he acted quickly enough; he'd just been so desperate to try _anything _to escape his apparent destiny that he hadn't taken the Grandfather's own resources into account._

_He'd underestimated himself, and now his people would pay the price…_

_He had only just registered someone coming towards him when he suddenly found himself yanked backwards, landing on the ground in the middle of a very familiar console room._

"_Compassion?" the Doctor said, looking around him in surprise at the sight of his latest TARDIS, so unexpectedly returned to him despite the Faction's reported control over her. "But-?"_

"_When the Faction jumped away from your attack, it broke their control over me; Nivet was forced out by the jolt, but I'm OK," Compassion's voice explained, her tone sounding slightly amused despite the grim reality of the situation facing them, even as the familiar sounds of materialisation filled her console room. "He's trying to send in ships to intercept the beam, but I'm managing to deflect them by stopping them getting too close-"_

"_You're _what_?" the Doctor said, eyes widening in horror as he ran to the nearest console screen to study the readouts before him; Compassion was deflecting the Faction ships by materialising in a location that they were travelling towards just before they could get there themselves. The Doctor had attempted something similar himself once, but that had been a last-ditch gambit dealing with an inferior time machine that wasn't meant to be there in the first place; this deliberate deflection was _impossibly _dangerous…_

"_Why are you _doing _this?" he asked, looking up at Compassion's ceiling in confusion. "The weapons are releasing enough power to annihilate this _constellation_-"_

"_But if the Faction can divert that energy they'll manage to spare Gallifrey from the worst of the assault," Compassion said grimly. "They might be good, but their options will be limited if we can keep them getting their hands on Gallifreyian technology…"_

_The Doctor couldn't even bring himself to argue with Compassion; no matter what he tried to do, he could never save enough Time Lords to make a difference now that the Faction had control of the Matrix, but if he could limit their power…_

"_Wait!" he said, a sudden thought to occurring to him. "Where's Fitz-?!"_

"_Right here," the voice of their other companion interrupted, Fitz Kriener staggering out of a nearby corridor to join them with a slightly shaky smile. "That was… interesting, huh?"_

"_Fitz…" the Doctor said, suddenly stuck for what he could say when faced with this version of his friend- it was one thing to talk about continuity and the role of memory in defining identity when he'd believed that the original Fitz was dead, but another thing altogether when he _saw _Fitz die in front of him…_

"_They got Romana," Fitz said, looking apologetically at the Doctor. "Compassion rescued me, but some of those bone guard things shot Romana and Mali as she was pulling me in…"_

"_Oh," the Doctor said, lost for anything else to say as he looked at his friend, momentarily unsure how to feel at that news._

_No matter what she'd become in this incarnation, Romana had still been his friend…_

"_Compassion!" he yelled, looking up at her once more, suddenly reminded of something that another old friend of his had once attempted to take from Gallifrey. "Don't forget the Eye-!"_

"_Already done," Compassion said, sounding amused at the thought that she'd beaten him to something. "Nivet had already established a direct link to the Eye in the hopes of shaking off the Faction's control by channelling its power directly into me; all I had to do was use that connection and cut off all other access to it… and before you say anything, all other TARDISes were still deactivated; even if they'd had access to the Eye, they couldn't have done anything."_

_The Doctor decided not to press that issue; judging by the amount of strain that Compassion was inflicting on herself right now, any additional power they could gain would be welcome, and he had to have faith that she would have saved other Time Lords if it was possible for her to do so. _

_As he grimly watched her screen, helpless to do anything else, the beam struck Gallifrey, Compassion's screens dimming as the explosion shook the cosmos around them even as she began to pull away, the explosion collapsing down into nothing almost as soon as the Doctor had processed it._

_That was why the Doctor hated weapons; they made it too easy to do what should be unthinkable..._

"_Found it!" Compassion yelled, suddenly enthusiastic once again. For a moment the Doctor was tempted to yell at her- what could be _good _about this situation?- but then he saw the small black box and felt the presence in his mind, and recognised it instantly._

_It was bruised, battered and damaged, but it was his TARDIS…_

"_How-?" he began._

"_My link to your ship and the Eye of Harmony still being connected to it; together, they were enough to find what we needed," Compassion explained._

"_That's the TARDIS?" Fitz said, looking at the tiny box uncertainly. "Uh… it used to be bigger, right?"_

"_It just expended a colossal amount of energy in one go; it needs time and power to recover," Compassion said briefly, before the central column began to move faster. "Just a moment… there's still time…"_

"_Time for what?" the Doctor said, looking uncertainly at the ceiling (He didn't want silence; with Compassion focusing on something else, the second Fitz asked him something he'd break down, horrified at the thought of what he was now inevitably destined to become…)._

"_This," Compassion said. The Doctor didn't even have time to ask what she was talking about before the console room suddenly shook around them, knocking him and Fitz into the console and prompting a brief grunt from Compassion._

"_Well," she said, her tone surprisingly satisfied, "that was a bit rougher than expected, but it's done now."_

"_Done?" the Doctor repeated. "What's done?"_

"_Nudging your past self's TARDIS out of range of the time corridor you created while you were in that cell," Compassion explained; she was actually starting to sound tired, despite the fact that she shouldn't be capable of fatigue in her current state. _

"_What?" the Doctor said, unable to believe what he'd heard; just when he was worry about his destiny…_

"_I restored your original third regeneration," Compassion confirmed. "The Grandfather's cut himself off from your timeline already as part of his Faction initiation rites, so he still exists, but you've now been cut off from his; as far as the rest of the universe is concerned, your time at Dust was just an interesting little possibility that never happened, and you are now no longer a victim of the Paradox biodata virus."_

"_Really?" the Doctor said, suddenly feeling a new sense of hope about his position._

_They might not have managed to pull it off in time to save Gallifrey, but if he was no longer destined to become the Grandfather, they might still be able to-_

_The console room suddenly shook as something struck Compassion from outside, the resulting explosion caused sparks to fly from one of Compassion's consoles as the Doctor hurried over to the controls. _

"_We're under attack," Compassion said grimly before the Doctor could ask the question himself._

"_The Faction?" Fitz asked._

"_Who else could it be?" Compassion pointed out, the floor beneath their feet shifting slightly as Compassion presumably moved to evade another attack. "They might not have War-TARDISes, but they know what they're doing, and they're converging on us."_

_The Doctor didn't need to wonder how that could be; after the Faction had demonstrated the ability to control Compassion via her old receiver, tracking that receiver's signal would be relatively easy, given their pre-existing access to it. _

"_Do we have any means of shaking them off?" he asked, desperately checking over Compassion's controls for something they might have missed; removing the receiver had been dismissed as impractical in the past, but maybe if he could find the controls for Compassion's chameleon circuit…_

"_Not as long as you're in me," Compassion said grimly. "But maybe… if I can divert enough power to your ship…"_

_Realising what she meant by that, the Doctor turned to look at the small black box once again, and couldn't restrain a slight smile at the sight of it growing to a more familiar size, the colour shifting back to the familiar reassuring blue and the box taking on its familiar dimensions…_

_It was only when he heard the groan from Compassion that the Doctor realised where the ship before him was getting its power from._

"_Compassion, _stop_!" he cried, looking desperately up at her; he'd already lost his planet, he couldn't lose his _companions_! "You'll-!"_

"_I've made my choice, Doctor," Compassion said, her tone firm even as a glance at the console monitors confirmed the Doctor's fears; Compassion's interior was being deleted as she channelled her own energy into the TARDIS, sacrificing whole parts of herself to accelerate the gradual healing process that his ship would have to undergo if left on its own. "The link to the Eye of Harmony has been modified so that only your ship can access it, and I've got enough residual energy to hold them back while you escape, but… well, if they can track me by my receiver…"_

"_You need me, don't you?" Fitz said, looking solemnly at the console before the Doctor could say anything._

"_Yes," Compassion said, sounding apologetic at what she was asking Fitz to do (If it had been any other occasion, the Doctor would have been grateful to hear such evidence of Compassion's expanding personal development, but now all he could think of was the fact that this was where it would all end). "I can direct you to the appropriate controls, but I can't risk attacking the Faction directly under my own power; if they manage to hack into my old receiver, they could regain control and turn me against you along with every other ship out there, but if Fitz is controlling me manually, he can override everything they try to make me do…"_

"_You don't have to-!" the Doctor began._

"_Fitz died a long time ago, Doctor," Fitz said, looking at his friend with that fearful courage that the Doctor had once been so proud of nurturing in his friend and now hated himself for bringing into Fitz's life; what was the point in encouraging his friends to develop if they ended up _dying_ for him? _"All I can do is make this count for something… and I choose to make this count by making sure you survive to give the Faction Hell."__

"_But-!" the Doctor began, before he suddenly felt Compassion's internal gravity shift as he fell backwards into his original TARDIS, the interior still not fully reformed but the essential details of the control console ready for him to steer the ship. For a moment, the Doctor thought about dashing back out to rejoin Fitz and Compassion, but when he saw Compassion flying away from the still-open doors, hurtling towards the approaching Faction ships, he abandoned that thought and turned his attention back to the regenerating console. _

_He was too far away to save them now, but if his friends were going to die for him, he was going to _live _for them…_

_With nothing else to do, he set the TARDIS in motion, smiling as he felt the old girl's familiar presence filling his mind- his link with Compassion had been interesting, but there'd always been that edge of hostility that this ship lacked-, trying to distract himself from the thought of what was happening behind him by focusing on what was now in front of him…_

"DOCTOR!_" a voice suddenly yelled, the Doctor glancing over at the newly-restored monitor to see the Grandfather glaring at him from the screen. "_How DARE you_-?"_

"_Prove you wrong?" the Doctor replied with a smile. "Get used to it, Grandfather; _everything _you knew about my future was wrong."_

"You destroyed Gallifrey _-!" the Grandfather began._

"_As well as claiming the Eye of Harmony, preventing you from getting your hands on any Time Lord technology, and escaping your entire fleet," the Doctor said, smiling mockingly at the Grandfather; after so much loss, focusing on what had been gained was important. "Oh, and Compassion and I just averted the moment when my third self went to Dust, so I'm sorry to say that the virus has still been removed from my system; it was a trickier approach, but it got the job done."_

"You think you've won because you erased that regeneration_?" the Grandfather said, looking scathingly at him. "_We still control the Web of Time now; you can't run forever, Doctor_!"_

"_Why not?" the Doctor asked, smirking as he looked at the Grandfather's image on the screen. "I've done it before."_

"You will be hunted by the Faction for all eternity_-!"his other self proclaimed._

"_And I just took away your access to Gallifrey's resources," the Doctor pointed out, his satisfaction at undermining the Faction's threat briefly allowing him to forget the pain he felt at the thought of what his other self had just reminded him of. "You might find me, but you'll find it very difficult; for all your talk about the power of the Faction, you can't fulfil most of your original plans without control of Time Lord technology, not unless you want to actually _destroy _everything. You may hate the structure of Web of Time, but you still can't want to unravel it completely; without what was on our homeworld, you can't be sure there'll be anything to knit back together later, after all."_

"I_ am_ you, Doctor-!_" the Grandfather yelled._

"_And not only would I not know how to do that, but I'm not going to do what you expect right now," the Doctor said, reaching down to activate the emergency boost system just underneath the console. "Goodbye, Grandfather; good luck trying to conquer reality with a planet's cast-offs."_

_With that said, he set the TARDIS into accelerated motion once again, hurtling through the vortex towards some unknown destination, the Faction's twisted TARDISes left lagging behind by the sheer power of the Doctor's own ship._

_For a moment, the Doctor stood in the middle of the console room and smiled at the sight of his old friend, the ship putting the last touches to the restored room as it completed its own regeneration after so many centuries of holding back the virus…_

_Then the weight of what had just happened struck him, and all the Doctor could do was fall to the floor, lean back against the console, and sob._

_He'd been manipulated into destroying his own planet… his companions had died to give him the chance to escape… he'd restored his oldest friend and saved his own timeline from contamination…_

_And he didn't know what to do next…_

* * *

><p>"So there you have it, Pond," the Doctor said, looking grimly over at Amy, the faint gleam of tears in his eyes at the memory of the events he had just recounted to her. "The Faction were created by a version of me that rejected everything I swore to stand for, I destroyed my own people in a blind moment of desperate arrogance because I thought I knew what to do, and I'm only still alive because the woman I'd sworn to protect and the man I considered my brother gave their lives to give me a chance to get away."<p>

"So… your people were taken out of the picture, and… without them to keep time travel under control… the Faction have been active ever since?" Amy asked (She _wasn't _going to think about what the Doctor had done; he'd taken a desperate gambit to save everything, and the fact that it hadn't worked out didn't change what he'd tried to accomplish).

"Essentially, yes," the Doctor confirmed. "Compassion's actions ensured that the Faction didn't have the time to recover any Gallifreyian technology before the blast I fired destroyed the planet, and they weren't able to get in touch with any of their agents on Gallifrey when it happened in time to get them to safety, but even with those losses, the Faction aren't to be sneezed at; they just have to be more subtle at manipulating the timelines than they'd like to be to avoid causing too many paradoxes…"

"They don't want to break reality and have nothing to do tomorrow, eh?" Amy said, trying to smile about it to lighten the Doctor's spirits without appearing too jocular; this topic was clearly difficult for him as it was.

"Exactly," the Doctor confirmed. "With access to Time Lord technology, they could have rewritten everything they wanted whenever they wanted it and moderated the side-effects of the changes, but without Gallifrey to pillage all they have is what they had before; they're still dangerous without the Time Lords to keep them in check, but the Grandfather's knowledge stops them from pushing reality too far…"

He sighed as he stared at the floor, not wanting to look at Amy as he continued to talk. "And I've tried to step in when I've found something big enough to be worth interfering in- the Kulan invasion in 2000, a Dalek fleet attacking Earth in the future, things like that- or when I was under direct attack already, like when I was chased by these shape-shifting assassins that wanted my DNA, but I've tried to stay low to avoid attracting the Faction's attention until I have a better plan, as well as keep people out of my life because of the danger they'd be in. I've only taken one person into the TARDIS for a long-term period since that day, and that was only because he would have died and didn't have anywhere else to go…"

"What… what happened to him?" Amy asked, as the Doctor's voice trailed off before he completed his sentence.

"He died helping me stop another invasion," the Doctor said grimly. "And I tried to save his life, and all I did was make it worse… I swore I'd never have another companion after that…"

Before Amy could say anything, he looked over at her with a soft, slightly tearful smile, and reached up to stroke her cheek, a tenderness about him that Amy couldn't recall her friend ever showing before. "But then… I staggered out of my ship after one of the most difficult moments of my lives, ready to begin a new life, and there you were… unafraid of the madman who fell out of his box and ate fish custard… willing to stand up and confront what I'd done to you in the middle of a terrifying situation… isolated and alone in a world surrounded by those who should have been your peers…"

He smiled warmly at her, noting the slight trace of tears in her own eyes at his reassuring words. "I may have been intrigued at the mystery of the crack… but I stayed because I realised that you gave me the kind of faith that I thought I didn't deserve any more, and I wanted to prove worthy of it."

"You never had to-" Amy began.

"But I did, Amelia," the Doctor said, his expression becoming more solemn as he looked at her. "I jumped over half your life and left you at the non-existent mercy of one of the Faction's lao spirits… I barely saved you and Earth from it… I left you to deal with ridicule simply because you believed in me…"

He shook his head at the memory. "I stayed for so many reasons, but it comes down to two; I wanted to make up to you for leaving you alone for so long, and I reasoned that the Faction were already aware of you after Prisoner Zero's actions, so it was best if I was there to prepare you for it."

"And… you're giving me the option to leave?" Amy said, looking at him uncertainly.

"You're prepared for the worst of what they could try and throw at you; the Faction are dangerous, but they're also subtle unless they're desperate or confident that the results would be worth it," the Doctor said, looking at her. "If you stay here, they may or may not come after you… but if you come with me, they could be anywhere, waiting for the moment when I'll reveal myself and they can make me one of them once more."

Having said what he had to say, the Doctor sat back and looked silently at his potential companion as she stared at him, her expression giving no indication of her thoughts as she studied him.

"That's what Marion meant at Poseidon Eight, wasn't it?" Amy said at last. "When you said that you're never going to be him any more, and Marion said that you would… they want you to join them?"

"The problem with going evil is that you think everyone should want to join you in being evil," the Doctor said, rolling his eyes at the thought before he became more serious. "Unfortunately, that just makes the Grandfather more dangerous; he no longer understands me or why I do what I do, but he remembers enough to know approximately how I will react under the right circumstances, and he will never stop hunting for me and the old girl to ensure control of the last parts of Gallifrey that remain. He's too powerful to confront directly, and there's only so much that I can do against the Faction and whatever plans I find… but if you come with me, we will fight them everywhere we find them, and we will do everything we can to preserve what should be."

After a moment's silence, Amy looked at him with a simple smile.

"I'm staying here," she said.

"You don't have to-" the Doctor began.

"I _want _to," Amy said, reaching out to place a hand on his cheek, directing his face so that he was gazing directly into her eyes. "I made my choice a long time ago, Doctor; I'm going to go with you."

"But the Grandfather-" the Doctor began.

"So I'll be a target of a deranged mass-murderer who knows everything you've done up to a certain point and won't stop until he's corrupted or killed you?" Amy asked, smiling teasingly at him. "I'm _definitely _not leaving you alone with someone like that after you; if you're going to fight him, I'm going to go with you."

Despite the grim story he'd just told her, the Doctor smiled as he gave Amy a thankful hug.

He'd shared his darkest secret with her, told her that he was the reason that the Faction had come to power, and she still accepted him…

* * *

><p>AN 2: To anyone wondering how the events here fit into the canon timeline, I'm assuming- based on revelations in 'Night of the Doctor' and 'Day of the Doctor'- that in the original continuity, the Doctor was able to restore Gallifrey after the events of 'The Ancestor Cell' (He discovered a means of doing so in the later novel 'The Gallifrey Chronicles'), but the restored Time Lords were then forced into war with the Daleks until the Doctors ended the War, resulting in the canon events that we know. With that in mind, assume that the Time War never happened, but the Faction's powers are still relatively limited compared to what they could have become as the Doctor destroyed Gallifrey before they could acquire anything useful from it, thus limiting what they can do to the universe without putting it and themselves in danger of non-existence (Reality can only take so much, after all).<p>

Anyway, hope you all liked that; next chapter concludes this story in the series, as Amy finally graduates and prepares to depart on her travels…


	29. Leaving Leadworth

Disclaimer: I don't own what you recognise; the drill should be familiar to you by now

Feedback: I'd appreciate it; I'm trying to do something a bit different here

AN: The last chapter, as Amy and the Doctor deal with their last business in Leadworth before departing (I wanted to upload this before the Eleventh Doctor regenerates); hope you like it

AN 2: In advance, I apologise if Amy comes across as cruel in her interaction with Rory; I'm trying to go for the idea that she's just never had a reason to look at him that way in Melody's absence, but I acknowledge that I might have failed to get the right balance

The History of Paradox

Standing in the clubhouse off the games field, looking at the rest of her year as they chatted amongst themselves in the school's post-graduation party- a small and simple thing, but a chance for the year heads to say goodbye- Amy couldn't stop herself from grinning.

She'd finally completed her school career, she'd passed all her exams, and she'd just had her graduation ceremony; even if Aunt Sharon was too busy with work to make it there herself, and even if she wasn't really talking to anyone else here, this day was _brilliant_!

Of course, it was when she turned to look out of the window at the sight of the blue box in a distant corner of the field that she remembered why she was particularly enthusiastic about this day; once she'd said her last goodbyes, she and the Doctor were on their way to the rest of the universe, and nothing was going to stand in their way.

Her actual courses may not have much relevance to what she was going out to experience in the wider universe, but she'd managed to focus on some interesting ones as well as have some fun. She'd tried to put in some extra work for the science courses, but there was only so much she could do with what a secondary school had to teach her, and English had been more about having fun with a good excuse to read some interesting books, even if history had been enjoyable beyond giving her some ideas about where she might want to go with the Doctor now. She'd even managed to successfully apply to a few universities with the Doctor's help, even if she'd concealed the response letters from her aunt; it would have just raised questions about why she was applying when Sharon didn't have the money to support her in a university course.

University might not be what she _really_ wanted to do with her life, but the point was that she had the option to go there and was still choosing to go with the Doctor; proving her abilities to herself was what really mattered right now…

"Uh… Amy?" a familiar voice said from the side.

"Rory!" Amy said, turning to grin at her friend as he walked up to her, an uncertainty about him that she couldn't place but decided not to worry about; if it was something she could help him with, Rory knew that he could ask her for help. "Can you believe it?"

"I know; who'd have thought we'd manage to get this far?" Rory said, smiling at her before his expression became suddenly awkward. "Look, Amy… there's something I wanted to say…"

"I've got something to say first," Amy said, looking apologetically at her friend; Rory was going to take this hard, but she had made her decision long ago, and she couldn't back out of it now. "Rory… I'm leaving Leadworth."

"Leaving Leadworth?" Rory said, looking at her in confusion, his initial apprehension forgotten. "But… we're all leaving-"

"I mean tonight," Amy said, hoping that her fragile 'cover story' would work; as much as she trusted Rory, with the Faction to worry about, the less people who knew that she'd left Earth with the Doctor, the better for everyone. "I'm… well, I met someone a while back, and we're… well, he likes to travel a lot, so…"

"You're… leaving Leadworth… with some guy you never told me about?" Rory said, looking at her with pain practically written all over his face (Amy knew that they were close, but she never thought that the fact that she hadn't mentioned a relationship would be that big a deal to him). "I thought… well-"

"I'm sorry, Rory," Amy said, smiling apologetically at him; she'd never found the right time to tell him about the Doctor, and now she never would, but this wasn't the time to get lost in the past. "I just never found a good moment to tell you about him, it wasn't anything personal…"

Stuck for anything else to say, she smiled encouragingly at him. "But hey; now that I'm not holding you back, you've got a chance to find someone, haven't you?"

"Uh… right," Rory said, nodding at her with a deliberately blank expression that Amy didn't need her long experience with her friend to know meant that he was trying to hide something.

If it had been any other day, she might have tried to press Rory about whatever he wasn't saying, but looking at him like that, evidently trying to hide the fact that she'd done something to cause him pain…

The fact that he turned around and walked off to the nearest toilets before she could ask him what was wrong made it easier; whatever was wrong was obviously going to be uncomfortable for both of them to discuss, but if he'd left the room, she could use the opportunity to do the same.

Maybe she was a coward, but Amy didn't want to stick around after that; she'd said her goodbyes to Rory, there was nobody else here she was particularly bothered about when faced with the possibility that she'd never see them again, and staying here would just mean that she'd run the risk of having to see Rory looking like… like _that_.

She'd known it would hurt him when she left, but they couldn't just keep on playing it safe by spending all their time together; she was ready to move on to bigger things with the Doctor, but that meant that Rory would have the chance to move on with his life as well.

"Goodbye," she said, looking after her only schoolfriend with a small, sad smile, before she turned and headed for the exit as discreetly as possible.

School had been an experience, but she was _more _than ready for this part of her life to be over and done with…

* * *

><p>As he stood outside the TARDIS waiting for Amy to leave her graduation after-party, the Doctor was amazed at how smoothly this was going.<p>

Taking companions had always been a relatively impulsive decision in the past- either they decided to join to get away from it all or they ended up stuck with him by accident when he couldn't get them back- and with the exception of his time in UNIT, he'd never been able to really ease anyone into it before; they either got into the ship, saw the interior, and were generally too amazed to say no when he made the offer later, they made the relatively impulsive request to come along and the Doctor never had the hearts to say no, or they never saw the inside because he was never interested in taking them along. Amy was the first occasion where he'd really put time and effort into training someone to be a companion- Jo didn't count as he was training her as a scientist first and foremost rather than a time-traveller; even if she'd enjoyed her time with him, Jo was an employee of UNIT first and foremost- but even if he'd surprised himself when he came up with the plan, in the end, he'd actually rather enjoyed the experience.

Leadworth might have been relatively boring, and he'd been forced to limit his interaction with his friends in this timeline- Sarah and Sam in particular weren't that far away in this time, but he couldn't afford to give the Faction too many clues about where he was by visiting old companions; even his initial chat with the Brigadier had been a risk- but it had been rather relaxing to not have to worry about finding somewhere safe to recuperate, giving him a chance to think and take his time while instructing Amy in what she would need to know when they started travelling together full-time.

It might have been an ironic way to feel considering his own attitude towards his studies- he was proud of his rank as a Time Lord, but he never fully saw the point of the attached status it gave him back on Gallifrey beyond the fact that it gave him the right to own the TARDIS- but as he had stood silently at the back of the school hall, a TARDIS key around his neck generating a low-level perception filter to stop anyone noticing him, watching Amy walk up and receive her graduation certificate, the Doctor couldn't help but feel proud at all that she had accomplished since his return to her life. His own training with her had gone well, focusing on the essentials that any time-traveller would have to know, but he just felt proud of how well she'd handled conventional subjects on top of everything he had to teach her; he'd _never _been able to focus on his expected studies like that back on Gallifrey (Although that might have been because he had to spend so much time looking for things whereas he and Amy knew what they were trying to learn about)…

He didn't know what it was about Amelia Pond that made him feel so relaxed about taking on a new companion and preparing to take on a more active role once again, but now, for the first time since Gallifrey had been destroyed, he didn't feel afraid of the Faction any more.

That fear had driven him to force his own regeneration after he'd taken such a desperate gambit to stop the Vore from invading Earth after the TARDIS was damaged, had sent him on the run on his own to avoid subjecting anyone else to the life that he now had to live, had prompted him to avoid taking action wherever he went in case he attracted the Faction's attention…

No more.

The Doctor was firm on that decision; he wouldn't allow his fear to control him any more.

No matter the risks of travelling with him, Amelia Pond had chosen to remain with him, and he was not going to let down her faith in him by giving up so easily, regardless of how much the Grandfather still secretly scared him…

"I'm ready," Amy said, her voice bringing the Doctor's thoughts back to the present as his latest companion walked up to the TARDIS, smiling anxiously at him as she subtly adjusted her dark school uniform.

"You're not planning on wearing that full-time, are you?" the Doctor asked, indicating Amy's uniform with a slight smile; he might be committed to standing up and fighting back now, but anything that stopped him thinking of the Grandfather was a good thing in his book. "It might have worked for Turlough, but considering what he went through it just creates negative connotations…"

"Don't worry, I'm not going to travel with you permanently wearing my school uniform," Amy said, grinning at her friend as he opened the door and waved her into the ship (And no, he did _not _sneak a look at her as she went in; this was _Amelia Pond _he was looking at, she'd been through enough without… _that_). "But just to be sure, you _did _pick up my bags, right?"

"All stowed away in your room, Pond," the Doctor said, smiling at her as he closed the door behind him, before he reached over to turn Amy around so that she was facing him directly, his hands on her hsoulders as he looked at her.

"Amelia Pond," he said, hoping that the full name would emphasise the seriousness of what he was about to say, "for the last time, you're _sure _this is what you want? I can't guarantee your safety, and I can't be sure what we'll find out there-"

"And I don't care about that," Amy interjected, placing a finger on the Doctor's lips as she smiled at him (And he did _not _sniff her finger). "I know the risks, Doctor, and I'm still here; after everything you've told me, I want to see what's out there. Maybe it's dangerous, but it's dangerous for the right reasons."

"It's fun?" the Doctor said, smiling slightly at her as she lowered her finger.

"It's fun, it's incredible, it lets me see things nobody else could ever imagine seeing… and we make a difference," Amy said, looking solemnly back at him before she gave him a warm, encouraging smile. "I know it's a risk, Doctor… but if it gives me the chance to do all that, it's a risk I want to take."

Smiling gratefully back at her, the Doctor stepped back, raised one hand, and snapped his fingers, the TARDIS door swinging open behind him, allowing him and Amy to walk into the ship. The Doctor noted with a slight smile that the central time rotor almost seemed to be glowing brighter than normal, as though it wanted to mark Amy's first time entering the ship as a full-time companion rather than a 'student' on a temporary 'trip', but Amy didn't seem to notice, focusing instead on the thought of what awaited them as they walked up to the control console.

"Right then," the Doctor said, checking to make sure that the door was closed behind them before he turned his attention back to Amy, "the TARDIS has moved all your things to your new room, and I've made arrangements with UNIT to back up your cover story if your aunt tries to check it out- they call it 'backstopped', apparently; if she tries to call you someone will just say that you're out or otherwise occupied- so she'll never have any reason to think that you're anywhere that you shouldn't be until you're ready to tell her."

"What happened to you being able to have me back five minutes from now?" Amy asked with a teasing smile.

"Well, you've got to allow for some piloting errors; the Vortex isn't what it used to be these days…" the Doctor said defensively, patting the TARDIS console as though trying to sooth its wounded feelings.

"Don't worry about it," Amy said, copying the Doctor's affectionate pat to the console. "I'm not really planning to come back any time soon; if you've got a cover story prepared, that's fine with me.

"Ah, good," the Doctor said, reaching over to take Amy's hand and place it on the dematerialisation lever. "Well then, with that straightened out, if you would care to do the honours, Amelia Pond?"

"Me?" Amy said, grinning despite the simplicity of the task as she eagerly looked over the console's current settings. "Where are we going?"

"No idea," the Doctor grinned. "Coordinates are set to shuffle, so we could wind up anywhere; past, present, future, distant planet, attached pocket universe… the possibilities are endless."

"Good," Amy said, taking a deep breath as she looked at the lever in her hands, the grin on her face reflecting the Doctor's own feelings at the thought of resuming his travels. "In that case… goodbye, Leadworth; hello, universe!"

"_Geronimo_!" the Doctor yelled as Amy threw the lever forward to set the ship in motion, the central column rising and falling once again as the TARDIS departed, heading out into the universe once again, Leadworth vanishing from their surroundings as they headed out into the universe.

He didn't know where he and Amy were going to go in this new stage of his travels, he had no idea what would happen when they next faced the Faction, and he was dreading the possibility of confronting the Grandfather once more…

But now, for the first time since that dark day when he'd been tricked into destroying Gallifrey and been left on the run from his own twisted counterpart and the remains of his own people, as he stood in the TARDIS with Amelia Pond by his side, the Doctor actually _felt _like himself again…

* * *

><p>AN 3: Well, there you have it; next time I return to this series- in an all-new story, so keep an eye out- we will be exploring 'the World of Paradox', as the Doctor and Amy meet some newold friends and learn more about the universe that exists under the control of Faction Paradox…


End file.
